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/7769584/working' mkdir: created directory `/scratch/stefan/7769584/working/protonate' Storing results in /scratch/stefan/7769584/finished Working in /scratch/stefan/7769584/working /scratch/stefan/7769584/working /scratch/stefan/7769584 /scratch/stefan/7769584/working/protonate /scratch/stefan/7769584/working /scratch/stefan/7769584 Precomputing protomers for all compounds (pH: 7.4) /nfs/soft/jchem/jchem-19.15/bin/molconvert: line 38: /nfs/home/stefan/.install4j: No such file or directory /nfs/soft/jchem/jchem-19.15/bin/molconvert: line 39: 7: Bad file descriptor /nfs/soft/jchem/jchem-19.15/bin/cxcalc: line 38: /nfs/home/stefan/.install4j: No such file or directory /nfs/soft/jchem/jchem-19.15/bin/cxcalc: line 39: 7: Bad file descriptor awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file Nov 27, 2019 6:16:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:22:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:23:16 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:16 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:16 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:16 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:22 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:22 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:22 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:22 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:22 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:23:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:43 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:44 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:44 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:44 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:44 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:44 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:45 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:45 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:45 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:45 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:23:45 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation ph 7.4: 1142 protomers created Coalesing and merging protomers 1112 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1117 protomers after new stereo-center expansion /scratch/stefan/7769584/working /scratch/stefan/7769584 Bulk generating 3D conformations all protomers in /scratch/stefan/7769584/working/3D mkdir: created directory `/scratch/stefan/7769584/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769584/working/protonate/xaaaaad-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' 1118 3D conformations generated for 1000 compounds Building REAL300000003001 mkdir: created directory `/scratch/stefan/7769584/working/building' mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003001' /scratch/stefan/7769584/working/building/REAL300000003001 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003001 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003001/0 /scratch/stefan/7769584/working/building/REAL300000003001 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1 `/scratch/stefan/7769584/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1) `REAL300000003001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003001 none O=C([O-])C1=CC=C(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 17, 17] 17 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 22 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003001 none O=C([O-])C1=CC=C(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 9, 9] 17 rigid atoms, others: [32, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 22, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 33, 34, 35, 40, 41]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003001 none O=C([O-])C1=CC=C(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 9, 9, 9, 9, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003001 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003001 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `/scratch/stefan/7769584/finished' Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003001/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003001 Building REAL300000003002 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003002' /scratch/stefan/7769584/working/building/REAL300000003002 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003002 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003002/0 /scratch/stefan/7769584/working/building/REAL300000003002 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/2 `/scratch/stefan/7769584/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2CCN(C3=CC=CC=C3)C2)C=C1) `REAL300000003002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003002 none O=C([O-])C1=CC=C(N=NCC2CCN(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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, 77, 78, 78, 76, 76, 22, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 78, 78, 78, 78, 22, 22, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 78, 78] 78 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003002 none O=C([O-])C1=CC=C(N=NCC2CCN(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [66, 60, 66, 60, 66, 66, 57, 57, 10, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 66, 66, 66, 66, 10, 10, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 1, 1, 66, 66] 78 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 159 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: REAL300000003002 none O=C([O-])C1=CC=C(N=NCC2CCN(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 36, 70, 70, 70, 70, 79, 79, 79, 79, 79, 70, 1, 1, 1, 1, 36, 36, 70, 70, 70, 70, 70, 79, 79, 79, 79, 79, 70, 70, 1, 1] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 230 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003002 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003002 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003002/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003002 Building REAL300000003003 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003003' /scratch/stefan/7769584/working/building/REAL300000003003 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003003 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003003/0 /scratch/stefan/7769584/working/building/REAL300000003003 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/3 `/scratch/stefan/7769584/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC(CCC(F)(F)F)CCC(F)(F)F)C=C1) `REAL300000003003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003003 none O=C([O-])C1=CC=C(N=NC(CCC(F)(F)F)CCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 18, 44, 47, 47, 47, 47, 18, 44, 47, 47, 47, 47, 1, 1, 1, 1, 18, 44, 44, 47, 47, 44, 44, 47, 47, 1, 1] 55 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003003 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003003 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003003/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003003 Building REAL300000003004 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003004' /scratch/stefan/7769584/working/building/REAL300000003004 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003004 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003004/0 /scratch/stefan/7769584/working/building/REAL300000003004 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/4 `/scratch/stefan/7769584/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC(F)F)C=C1) `REAL300000003004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003004 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [43, 29, 43, 29, 43, 43, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 43, 43, 43, 43, 29, 9, 1, 1, 1, 29, 43, 43] 61 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL300000003004 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 38, 38, 79, 79, 79, 39, 79, 79, 79, 144, 156, 156, 1, 1, 1, 1, 10, 38, 79, 46, 79, 156, 1, 1] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003004 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003004 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003004/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003004 Building REAL300000003005 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003005' /scratch/stefan/7769584/working/building/REAL300000003005 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003005 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003005/0 /scratch/stefan/7769584/working/building/REAL300000003005 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/5 `/scratch/stefan/7769584/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=C(Cl)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003005 none CCC(CC1=CC=C(Cl)C=C1)N=NC1=CC=C(C(=O)[O-])C=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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 4, 22, 42, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 22, 42, 42, 50, 50, 50, 50, 1, 1, 1, 1] 51 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 274 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: REAL300000003005 none CCC(CC1=CC=C(Cl)C=C1)N=NC1=CC=C(C(=O)[O-])C=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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 50, 50, 37, 38, 50, 50, 50, 50, 18, 18, 18, 18, 18, 9, 3, 3, 1, 1, 1, 1, 50, 50, 50, 50] 51 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 230 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003005 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003005 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003005/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003005 Building REAL300000003006 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003006' /scratch/stefan/7769584/working/building/REAL300000003006 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003006 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003006/0 /scratch/stefan/7769584/working/building/REAL300000003006 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/6 `/scratch/stefan/7769584/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1) `REAL300000003006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003006 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC(C)C2=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 101, 101, 195, 201, 201, 195, 201, 201, 201, 201, 201, 18, 36, 36, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 36, 36, 101, 101, 101, 195, 201, 201, 201, 201, 36, 36, 4, 4, 4, 4, 1, 1, 1, 1, 1, 36, 36] 201 rigid atoms, others: [42, 43, 44, 45, 46, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 632 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003006 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC(C)C2=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 64, 32, 34, 64, 64, 64, 64, 1, 1, 1, 1, 1, 11, 26, 26, 36, 36, 26, 36, 36, 1, 1, 6, 6, 6, 32, 64, 64, 64, 64, 1, 1, 26, 26, 26, 26, 36, 36, 26, 36, 36, 1, 1] 201 rigid atoms, others: [1, 36, 37, 48, 47, 13, 14, 15, 16, 17, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 462 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: REAL300000003006 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC(C)C2=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 64, 64, 26, 38, 167, 201, 201, 201, 201, 201, 201, 201, 64, 64, 21, 21, 21, 5, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 11, 12, 35] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 540 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003006 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003006 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003006/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003006 Building REAL300000003007 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003007' /scratch/stefan/7769584/working/building/REAL300000003007 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003007 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003007/0 /scratch/stefan/7769584/working/building/REAL300000003007 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/7 `/scratch/stefan/7769584/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC(Br)=C1) `REAL300000003007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003007 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 44, 57, 57, 44, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 44, 57, 57, 57, 57, 1, 1, 1] 57 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 200 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003007 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 57, 57, 57, 57, 57, 57, 30, 30, 30, 6, 1, 1, 1, 1, 57, 57, 57] 57 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003007 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003007 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003007/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003007 Building REAL300000003008 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003008' /scratch/stefan/7769584/working/building/REAL300000003008 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003008 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003008/0 /scratch/stefan/7769584/working/building/REAL300000003008 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/8 `/scratch/stefan/7769584/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(Cl)C(C(F)(F)F)=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003008 none CC(CC1=CC=C(Cl)C(C(F)(F)F)=C1)N=NC1=CC=C(C(=O)[O-])C=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.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 38, 70, 70, 42, 70, 70, 70, 70, 70, 70, 70, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 38, 38, 70, 70, 70, 1, 1, 1, 1] 70 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003008 none CC(CC1=CC=C(Cl)C(C(F)(F)F)=C1)N=NC1=CC=C(C(=O)[O-])C=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.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 69, 69, 70, 70, 70, 70, 70, 70, 70, 70, 17, 17, 17, 17, 7, 7, 1, 1, 1, 70, 70, 70, 70] 70 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 13, 31] set([0, 1, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003008 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003008 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003008/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003008 Building REAL300000003009 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003009' /scratch/stefan/7769584/working/building/REAL300000003009 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000003009 as failed and skipping /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `/scratch/stefan/7769584/failed' `/scratch/stefan/7769584/working/building/REAL300000003009' -> `/scratch/stefan/7769584/failed/REAL300000003009' Building REAL300000003010 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003010' /scratch/stefan/7769584/working/building/REAL300000003010 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003010 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003010/0 /scratch/stefan/7769584/working/building/REAL300000003010 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/9 `/scratch/stefan/7769584/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(C)(CN=NC2=CC=C(C(=O)[O-])C=C2)CC1) `REAL300000003010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003010 none CCOC(=O)N1CCC(C)(CN=NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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, 7, 7] 0 hydrogens need 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, 171, 134, 171, 134, 134, 131, 31, 131, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 201, 201, 134, 134, 134, 133, 134, 134, 134, 31, 31, 1, 1, 1, 1, 133, 133, 134, 134] 201 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) 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: REAL300000003010 none CCOC(=O)N1CCC(C)(CN=NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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, 7, 7] 0 hydrogens 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, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 66, 66, 133, 133, 79, 86, 134, 133, 133, 133, 1, 1, 45, 45, 45, 44, 44, 1, 1, 1, 1, 2, 2, 2, 9, 9, 133, 134, 133, 133, 1, 1, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 43, 44, 45, 42, 22, 23, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003010 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003010 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003010/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003010 Building REAL300000003011 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003011' /scratch/stefan/7769584/working/building/REAL300000003011 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003011 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003011/0 /scratch/stefan/7769584/working/building/REAL300000003011 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/10 `/scratch/stefan/7769584/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)C=C1) `REAL300000003011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003011 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 5, 1, 1, 1, 9, 9] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003011 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 1, 1] 9 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003011 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003011/1 /scratch/stefan/7769584/working/building/REAL300000003011 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/11 `/scratch/stefan/7769584/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)C=C1) `REAL300000003011.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003011 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', '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, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 7, 1, 1, 2, 1, 11, 11] 22 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 29] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 28, 30, 31]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003011 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', '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, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 22, 11, 1, 1] 22 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003011 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003011 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003011/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003011/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003011 Building REAL300000003012 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003012' /scratch/stefan/7769584/working/building/REAL300000003012 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003012 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003012/0 /scratch/stefan/7769584/working/building/REAL300000003012 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/12 `/scratch/stefan/7769584/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CCCC3)=C2)C=C1) `REAL300000003012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003012 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CCCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 112, 84, 112, 112, 84, 30, 30, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 112, 112, 112, 112, 84, 30, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 112, 112] 112 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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, 39, 40, 41]) total number of confs: 394 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003012 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CCCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [75, 47, 75, 47, 75, 75, 47, 12, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 75, 75, 75, 75, 47, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 76, 76] 112 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 316 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: REAL300000003012 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CCCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 38, 38, 76, 76, 38, 76, 76, 112, 112, 112, 112, 76, 1, 1, 1, 1, 12, 38, 76, 76, 38, 112, 112, 112, 112, 112, 112, 112, 112, 112, 76, 1, 1] 112 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 338 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003012 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003012 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003012/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003012 Building REAL300000003013 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003013' /scratch/stefan/7769584/working/building/REAL300000003013 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003013 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003013/0 /scratch/stefan/7769584/working/building/REAL300000003013 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/13 `/scratch/stefan/7769584/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(O)C(C(C)(C)C)=C1) `REAL300000003013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003013 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(O)C(C(C)(C)C)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 4, 7, 7, 7, 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 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 28, 6, 1, 1, 1, 1, 86, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 86 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 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: 152 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: REAL300000003013 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(O)C(C(C)(C)C)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 4, 7, 7, 7, 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 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 6, 6, 27, 43, 43, 27, 27, 43, 43, 43, 43, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 6, 27, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 86 rigid atoms, others: [1, 2, 3, 4, 5, 45, 17, 18, 19, 20, 24, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 176 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003013 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003013 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003013/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003013 Building REAL300000003014 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003014' /scratch/stefan/7769584/working/building/REAL300000003014 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003014 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003014/0 /scratch/stefan/7769584/working/building/REAL300000003014 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/14 `/scratch/stefan/7769584/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1) `REAL300000003014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003014 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 37, 56, 31, 56, 56, 30, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 56, 56, 56, 56, 30, 10, 1, 1, 1, 56, 56] 56 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000003014 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 27, 27, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 9, 27, 57, 57, 57, 1, 1] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003014 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003014 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003014/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003014 Building REAL300000003015 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003015' /scratch/stefan/7769584/working/building/REAL300000003015 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003015 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003015/0 /scratch/stefan/7769584/working/building/REAL300000003015 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/15 `/scratch/stefan/7769584/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F) `REAL300000003015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003015 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 82, 125, 82, 82, 82, 39, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 125, 125, 125, 82, 81, 38, 6, 1, 1, 1, 1, 82] 125 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003015 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 10, 10, 60, 81, 81, 69, 73, 81, 81, 81, 81, 1, 1, 1, 12, 12, 12, 1, 1, 10, 60, 81, 81, 81, 81, 1] 125 rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003015 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003015 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003015/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003015 Building REAL300000003016 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003016' /scratch/stefan/7769584/working/building/REAL300000003016 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003016 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003016/0 /scratch/stefan/7769584/working/building/REAL300000003016 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/16 `/scratch/stefan/7769584/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=NN(C)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1) `REAL300000003016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003016 none CN1C=C(C2=NN(C)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 125, 125, 125, 125, 125, 125, 44, 44, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 182, 182, 182, 182, 182, 182, 125, 125, 125, 125, 44, 7, 1, 1, 1, 1, 182] 182 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 274 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003016 none CN1C=C(C2=NN(C)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 84, 125, 125, 86, 116, 125, 125, 125, 125, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 13, 84, 125, 125, 125, 125, 13] 182 rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 454 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003016 none CN1C=C(C2=NN(C)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 65, 65, 151, 182, 182, 152, 182, 182, 182, 182, 182, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 65, 151, 182, 182, 182, 182, 1] 182 rigid atoms, others: [0, 1, 2, 3, 4, 38, 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, 35, 36, 37]) total number of confs: 582 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003016 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003016 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003016/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003016 Building REAL300000003017 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003017' /scratch/stefan/7769584/working/building/REAL300000003017 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003017 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003017/0 /scratch/stefan/7769584/working/building/REAL300000003017 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/17 `/scratch/stefan/7769584/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003017 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 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, 63, 63, 63, 63, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 106, 106, 63, 63, 16, 16, 1, 1, 1, 1] 106 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003017 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 15, 9, 1, 1, 1, 1, 1, 1, 8, 50, 50, 62, 62, 50, 50, 62, 62, 62, 62, 1, 9, 9, 1, 1, 8, 8, 62, 62, 62, 62] 106 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 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/7769584/working/building/REAL300000003017 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003017/1 /scratch/stefan/7769584/working/building/REAL300000003017 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/18 `/scratch/stefan/7769584/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003017.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003017 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 23, 23, 23, 23, 20, 20, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 36, 36, 23, 23, 20, 6, 1, 1, 1, 1] 36 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003017 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [18, 10, 19, 10, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 23, 12, 12, 23, 23, 23, 23, 1, 10, 10, 1, 1, 4, 12, 23, 23, 23, 23] 36 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003017 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003017 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003017/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003017/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003017 Building REAL300000003018 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003018' /scratch/stefan/7769584/working/building/REAL300000003018 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003018 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003018/0 /scratch/stefan/7769584/working/building/REAL300000003018 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/19 `/scratch/stefan/7769584/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C1) `REAL300000003018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003018 none CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C1 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 194, 129, 82, 129, 82, 82, 82, 82, 82, 82, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 82, 82, 82, 194, 194, 194, 194, 194, 194, 194, 194, 194, 82, 82, 82, 82, 82, 82, 33, 7, 1, 1, 1, 1, 82, 82, 82] 194 rigid atoms, others: [48, 49, 46, 47, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52]) 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: REAL300000003018 none CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C1 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 82, 82, 52, 52, 82, 82, 82, 82, 1, 1, 1, 14, 14, 14, 13, 13, 13, 14, 14, 14, 1, 1, 1, 1, 1, 1, 10, 52, 82, 82, 82, 82, 1, 1, 1] 194 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 40, 50, 51, 52, 43, 41, 26, 27, 28, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003018 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003018 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003018/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003018 Building REAL300000003019 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003019' /scratch/stefan/7769584/working/building/REAL300000003019 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003019 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003019/0 /scratch/stefan/7769584/working/building/REAL300000003019 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/20 `/scratch/stefan/7769584/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1) `REAL300000003019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003019 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 173, 201, 201, 173, 76, 76, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 201, 201, 201, 201, 173, 76, 22, 22, 1, 1, 1, 1, 22, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003019 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 60, 90, 56, 90, 90, 54, 7, 7, 1, 1, 1, 1, 1, 1, 8, 22, 22, 8, 8, 22, 22, 1, 1, 90, 90, 90, 90, 54, 7, 1, 1, 22, 22, 22, 22, 1, 90, 90] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38]) total number of confs: 408 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003019 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 10, 38, 38, 90, 90, 90, 90, 191, 201, 201, 191, 191, 201, 201, 90, 90, 1, 1, 1, 1, 10, 38, 90, 90, 201, 201, 201, 201, 90, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003019 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003019 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003019/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003019 Building REAL300000003020 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003020' /scratch/stefan/7769584/working/building/REAL300000003020 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003020 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003020/0 /scratch/stefan/7769584/working/building/REAL300000003020 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/21 `/scratch/stefan/7769584/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)C=C1) `REAL300000003020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003020 none O=C([O-])C1=CC=C(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 77, 93, 77, 93, 93, 77, 29, 29, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 93, 93, 93, 93, 77, 29, 5, 1, 1, 1, 1, 93, 93] 93 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 330 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003020 none O=C([O-])C1=CC=C(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [77, 53, 77, 53, 77, 77, 53, 10, 10, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 76, 77, 77, 77, 52, 10, 1, 5, 5, 2, 5, 76, 76] 93 rigid atoms, others: [9, 10, 11, 12, 13, 14, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003020 none O=C([O-])C1=CC=C(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 11, 35, 35, 79, 79, 79, 79, 93, 93, 93, 93, 93, 93, 79, 1, 1, 1, 1, 11, 35, 79, 93, 93, 93, 93, 1, 1] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003020 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003020 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003020/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003020 Building REAL300000003021 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003021' /scratch/stefan/7769584/working/building/REAL300000003021 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003021 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003021/0 /scratch/stefan/7769584/working/building/REAL300000003021 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/22 `/scratch/stefan/7769584/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C) `REAL300000003021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003021 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 2, 2, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 47, 117, 117, 64, 117, 117, 117, 117, 117, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 17, 17, 9, 9, 9, 47, 117, 117, 117, 117, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 140 rigid atoms, others: [1, 34, 35, 36, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 445 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: REAL300000003021 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 2, 2, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 117, 117, 117, 117, 117, 117, 117, 117, 117, 140, 140, 140, 31, 31, 31, 7, 1, 1, 1, 1, 117, 117, 117, 140, 140, 140, 140, 140, 140, 140] 140 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 11, 12, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003021 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003021 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003021/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003021 Building REAL300000003022 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003022' /scratch/stefan/7769584/working/building/REAL300000003022 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003022 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003022/0 /scratch/stefan/7769584/working/building/REAL300000003022 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/23 `/scratch/stefan/7769584/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1) `REAL300000003022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003022 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 29, 39, 39, 30, 30, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 39, 39, 40, 40, 1, 1, 1, 1] 40 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 163 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003022 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 40, 40, 40, 40, 40, 40, 40, 39, 22, 22, 22, 5, 1, 1, 1, 1, 40, 40, 40, 39] 40 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/7769584/working/building/REAL300000003022 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003022/1 /scratch/stefan/7769584/working/building/REAL300000003022 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/24 `/scratch/stefan/7769584/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1) `REAL300000003022.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003022 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 35, 35, 36, 36, 35, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 36, 36, 36, 36, 1, 1, 1, 1] 36 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003022 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 36, 36, 36, 36, 36, 36, 36, 36, 17, 17, 17, 17, 1, 1, 1, 1, 36, 36, 36, 36] 36 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003022 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003022 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003022/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003022/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003022 Building REAL300000003023 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003023' /scratch/stefan/7769584/working/building/REAL300000003023 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003023 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003023/0 /scratch/stefan/7769584/working/building/REAL300000003023 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/25 `/scratch/stefan/7769584/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=CC=CC=C2)=C1) `REAL300000003023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003023 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [28, 4, 28, 81, 81, 83, 83, 81, 81, 83, 83, 83, 83, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 28, 28, 28, 28, 83, 83, 83, 83, 4, 4, 4, 1, 1, 1, 1, 1, 4] 83 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: 178 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003023 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 72, 72, 83, 83, 72, 72, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 13, 13, 13, 13, 83, 83, 83, 83, 2, 2, 2, 4, 4, 3, 4, 4, 1] 83 rigid atoms, others: [1, 41, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000003023 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [26, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 26, 26, 26, 26, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83] 83 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003023 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003023 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003023/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003023 Building REAL300000003024 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003024' /scratch/stefan/7769584/working/building/REAL300000003024 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003024 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003024/0 /scratch/stefan/7769584/working/building/REAL300000003024 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/26 `/scratch/stefan/7769584/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CSC(C(F)(F)F)=C2)C=C1) `REAL300000003024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003024 none O=C([O-])C1=CC=C(NN=CC2=CSC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 40, 36, 40, 40, 36, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 40, 40, 40, 40, 36, 8, 1, 1, 40, 40] 40 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 20, 21, 22, 23, 24, 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: REAL300000003024 none O=C([O-])C1=CC=C(NN=CC2=CSC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 26, 26, 39, 39, 39, 39, 40, 40, 40, 39, 1, 1, 1, 1, 9, 26, 39, 39, 1, 1] 40 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003024 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003024 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003024/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003024 Building REAL300000003025 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003025' /scratch/stefan/7769584/working/building/REAL300000003025 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003025 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003025/0 /scratch/stefan/7769584/working/building/REAL300000003025 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/27 `/scratch/stefan/7769584/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(C(F)(F)F)SC=C2)C=C1) `REAL300000003025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003025 none O=C([O-])C1=CC=C(NN=CC2=C(C(F)(F)F)SC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 37, 32, 37, 37, 32, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 37, 37, 37, 37, 32, 9, 1, 1, 37, 37] 37 rigid atoms, others: [9, 10, 11, 12, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 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: REAL300000003025 none O=C([O-])C1=CC=C(NN=CC2=C(C(F)(F)F)SC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 8, 26, 37, 37, 1, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003025 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003025 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003025/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003025 Building REAL300000003026 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003026' /scratch/stefan/7769584/working/building/REAL300000003026 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003026 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003026/0 /scratch/stefan/7769584/working/building/REAL300000003026 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/28 `/scratch/stefan/7769584/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CCOCC2)C=C1) `REAL300000003026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003026 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 109, 125, 109, 125, 125, 109, 37, 37, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 109, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125] 125 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39]) total number of confs: 386 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003026 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 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: [95, 69, 95, 69, 95, 95, 69, 12, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 95, 95, 95, 95, 69, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 95, 95] 125 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 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: REAL300000003026 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 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, 1, 1, 11, 36, 36, 70, 70, 70, 70, 70, 93, 93, 93, 93, 93, 1, 1, 1, 1, 11, 36, 70, 70, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 24, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003026 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003026 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003026/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003026 Building REAL300000003027 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003027' /scratch/stefan/7769584/working/building/REAL300000003027 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003027 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003027/0 /scratch/stefan/7769584/working/building/REAL300000003027 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/29 `/scratch/stefan/7769584/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCC(C3=CC=CC=C3)CC2)C=C1) `REAL300000003027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003027 none O=C([O-])C1=CC=C(N=NC2CCCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 11] 11 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 17 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003027 none O=C([O-])C1=CC=C(N=NC2CCCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 10, 11, 11, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 11, 11] 11 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003027 none O=C([O-])C1=CC=C(N=NC2CCCC(C3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003027 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003027 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003027/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003027 Building REAL300000003028 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003028' /scratch/stefan/7769584/working/building/REAL300000003028 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003028 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003028/0 /scratch/stefan/7769584/working/building/REAL300000003028 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/30 `/scratch/stefan/7769584/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC(F)=C1F) `REAL300000003028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003028 none CN(C)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003028 none CN(C)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 16, 21, 21, 16, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 16, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 17, 18, 35, 20, 21, 22, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003028 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003028 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003028/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003028 Building REAL300000003029 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003029' /scratch/stefan/7769584/working/building/REAL300000003029 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003029 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003029/0 /scratch/stefan/7769584/working/building/REAL300000003029 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/31 `/scratch/stefan/7769584/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C(C)=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C=C1OC) `REAL300000003029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003029 none COC1=CC2=CC=C(C(C)=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 7, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 145, 149, 149, 149, 149, 149, 38, 38, 38, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 149, 149, 149, 149, 149, 188, 188, 188, 188, 149, 149, 149, 38, 38, 38, 7, 1, 1, 1, 1, 149, 149, 188, 188, 188] 188 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 364 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: REAL300000003029 none COC1=CC2=CC=C(C(C)=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 7, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 84, 149, 149, 84, 124, 149, 149, 149, 149, 1, 1, 1, 1, 1, 3, 4, 4, 4, 1, 1, 1, 13, 13, 13, 84, 149, 149, 149, 149, 1, 1, 3, 3, 3] 188 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 21, 22, 23, 24, 25, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 648 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003029 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003029 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003029/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003029 Building REAL300000003030 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003030' /scratch/stefan/7769584/working/building/REAL300000003030 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003030 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003030/0 /scratch/stefan/7769584/working/building/REAL300000003030 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/32 `/scratch/stefan/7769584/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl) `REAL300000003030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003030 none CC1=CC(O)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 22, 22, 18, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 44, 17, 5, 1, 1, 1, 1, 22] 44 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 98 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: REAL300000003030 none CC1=CC(O)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 22, 22, 21, 21, 22, 22, 22, 22, 1, 1, 1, 2, 2, 2, 1, 2, 7, 21, 22, 22, 22, 22, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003030 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003030 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003030/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003030 Building REAL300000003031 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003031' /scratch/stefan/7769584/working/building/REAL300000003031 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003031 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003031/0 /scratch/stefan/7769584/working/building/REAL300000003031 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/33 `/scratch/stefan/7769584/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)S2)C=C1) `REAL300000003031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003031 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 175, 197, 175, 197, 197, 175, 63, 63, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 175, 63, 13, 13, 1, 1, 197, 197] 197 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 620 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003031 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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: [122, 88, 122, 88, 122, 122, 88, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 122, 122, 122, 122, 88, 13, 1, 1, 13, 13, 122, 122] 197 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) 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: REAL300000003031 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 12, 44, 44, 95, 95, 95, 95, 95, 119, 119, 119, 119, 119, 1, 1, 1, 1, 12, 44, 95, 95, 119, 119, 1, 1] 119 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003031 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003031 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003031/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003031 Building REAL300000003032 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003032' /scratch/stefan/7769584/working/building/REAL300000003032 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003032 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003032/0 /scratch/stefan/7769584/working/building/REAL300000003032 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/34 `/scratch/stefan/7769584/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(F)=C2Cl)C=C1) `REAL300000003032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003032 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(F)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 41, 49, 41, 49, 49, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 41, 11, 1, 1, 49, 49] 49 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003032 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(F)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 49, 49, 49, 48, 49, 49, 49, 49, 1, 1, 1, 1, 9, 26, 49, 48, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003032 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003032 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003032/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003032 Building REAL300000003033 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003033' /scratch/stefan/7769584/working/building/REAL300000003033 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003033 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003033/0 /scratch/stefan/7769584/working/building/REAL300000003033 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/35 `/scratch/stefan/7769584/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1C(F)(F)F) `REAL300000003033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003033 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 2, 2, 7, 7, 7, 7, 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: [5, 1, 5, 5, 17, 21, 21, 17, 17, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 17, 21, 21, 21, 21, 1, 1, 1] 21 rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003033 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 21, 21, 21, 20, 21, 21, 21, 21, 21, 21, 20, 20, 20, 5, 1, 1, 1, 1, 21, 21, 21] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003033 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003033 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003033/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003033 Building REAL300000003034 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003034' /scratch/stefan/7769584/working/building/REAL300000003034 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003034 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003034/0 /scratch/stefan/7769584/working/building/REAL300000003034 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/36 `/scratch/stefan/7769584/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCC3=CC(F)=C(Cl)C=C32)C=C1) `REAL300000003034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003034 none O=C([O-])C1=CC=C(NN=C2CCC3=CC(F)=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 11, 11] 11 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24, 31]) total number of confs: 40 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: REAL300000003034 none O=C([O-])C1=CC=C(NN=C2CCC3=CC(F)=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 24 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003034 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003034 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003034/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003034 Building REAL300000003035 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003035' /scratch/stefan/7769584/working/building/REAL300000003035 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003035 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003035/0 /scratch/stefan/7769584/working/building/REAL300000003035 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/37 `/scratch/stefan/7769584/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(CC(C)C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003035 none CCC1=CC=C(C(CC(C)C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [88, 80, 38, 86, 86, 26, 26, 26, 46, 47, 47, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 86, 86, 88, 88, 88, 88, 88, 86, 86, 46, 46, 47, 47, 47, 47, 47, 47, 47, 7, 1, 1, 1, 1, 86, 86] 94 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 436 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: REAL300000003035 none CCC1=CC=C(C(CC(C)C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 12, 26, 28, 28, 12, 12, 60, 86, 86, 65, 76, 86, 86, 86, 86, 1, 1, 4, 4, 4, 4, 4, 1, 1, 26, 26, 28, 28, 28, 28, 28, 28, 28, 60, 86, 86, 86, 86, 1, 1] 94 rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 46, 22, 23, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 404 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003035 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003035 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003035/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003035 Building REAL300000003036 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003036' /scratch/stefan/7769584/working/building/REAL300000003036 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003036 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003036/0 /scratch/stefan/7769584/working/building/REAL300000003036 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/38 `/scratch/stefan/7769584/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl) `REAL300000003036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003036 none CC(C)OC1=CC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 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, 2, 2, 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, 79, 59, 79, 79, 79, 37, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 113, 113, 113, 113, 113, 113, 113, 79, 36, 6, 1, 1, 1, 1, 79] 113 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 274 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: REAL300000003036 none CC(C)OC1=CC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 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, 2, 2, 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: [17, 8, 17, 1, 1, 1, 1, 1, 1, 1, 10, 10, 47, 79, 79, 47, 47, 79, 79, 79, 79, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 10, 47, 79, 79, 79, 79, 1] 113 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 38, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 407 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003036 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003036 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003036/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003036 Building REAL300000003037 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003037' /scratch/stefan/7769584/working/building/REAL300000003037 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003037 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003037/0 /scratch/stefan/7769584/working/building/REAL300000003037 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/39 `/scratch/stefan/7769584/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1) `REAL300000003037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003037 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 157, 171, 157, 171, 171, 154, 60, 56, 8, 8, 38, 38, 8, 1, 1, 1, 1, 1, 1, 38, 38, 171, 171, 171, 171, 154, 56, 38, 38, 1, 1, 1, 1, 1, 1, 1, 38, 38, 171, 171] 171 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40]) total number of confs: 606 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003037 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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] 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: [68, 38, 68, 37, 68, 68, 37, 6, 6, 1, 1, 1, 1, 1, 1, 13, 38, 38, 38, 38, 1, 1, 68, 68, 68, 68, 37, 6, 1, 1, 38, 38, 38, 38, 38, 38, 38, 1, 1, 68, 68] 171 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 378 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: REAL300000003037 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3CCOC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 37, 37, 66, 66, 37, 58, 140, 169, 169, 169, 169, 66, 66, 1, 1, 1, 1, 10, 37, 66, 66, 169, 169, 169, 169, 169, 169, 169, 66, 66, 1, 1] 169 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 451 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003037 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003037 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003037/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003037 Building REAL300000003038 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003038' /scratch/stefan/7769584/working/building/REAL300000003038 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003038 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003038/0 /scratch/stefan/7769584/working/building/REAL300000003038 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/40 `/scratch/stefan/7769584/working/3D/40' -> `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(C(=O)[O-])C=C2)CC(C)(C)C1) `REAL300000003038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003038 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC(C)(C)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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 17, 23, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 17, 17, 17, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 34 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 88 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: REAL300000003038 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC(C)(C)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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 11, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 17, 17, 10, 10, 17, 16, 17, 17, 1, 1, 1, 1, 1, 12, 12, 12, 11, 11, 11, 12, 12, 12, 1, 1, 1, 1, 1, 17, 17, 17, 17, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 34 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 45, 46, 40, 53, 22, 23, 24, 25, 26, 54, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003038 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003038 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003038/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003038 Building REAL300000003039 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003039' /scratch/stefan/7769584/working/building/REAL300000003039 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003039 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003039/0 /scratch/stefan/7769584/working/building/REAL300000003039 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/41 `/scratch/stefan/7769584/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(O)C=CC=C3S2)C=C1) `REAL300000003039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003039 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(O)C=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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, 7, 7] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [37, 33, 37, 33, 37, 37, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 33, 11, 1, 2, 1, 1, 1, 37, 37] 74 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 27, 31]) 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: REAL300000003039 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(O)C=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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, 7, 7] 1 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, 8, 25, 26, 37, 37, 37, 37, 37, 37, 37, 36, 37, 1, 1, 1, 1, 8, 25, 37, 74, 37, 37, 37, 1, 1] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003039 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003039 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003039/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003039 Building REAL300000003040 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003040' /scratch/stefan/7769584/working/building/REAL300000003040 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003040 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003040/0 /scratch/stefan/7769584/working/building/REAL300000003040 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/42 `/scratch/stefan/7769584/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F) `REAL300000003040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003040 none CN(C)C1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 17, 17, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 7, 1, 1, 1, 1, 29] 29 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 56 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003040 none CN(C)C1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 29, 29, 23, 23, 28, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 6, 22, 29, 29, 29, 29, 1] 29 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 36, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003040 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003040 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003040/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003040 Building REAL300000003041 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003041' /scratch/stefan/7769584/working/building/REAL300000003041 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003041 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003041/0 /scratch/stefan/7769584/working/building/REAL300000003041 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/43 `/scratch/stefan/7769584/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=C(Br)C=C1F) `REAL300000003041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003041 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 15, 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, 2, 2, 7, 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: [12, 1, 12, 12, 37, 48, 48, 37, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 37, 48, 48, 48, 48, 1, 1] 48 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003041 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 15, 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, 2, 2, 7, 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: [27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 48, 48, 48, 48, 48, 48, 48, 48, 28, 28, 28, 5, 1, 1, 1, 1, 48, 48] 48 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003041 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003041 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003041/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003041 Building REAL300000003042 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003042' /scratch/stefan/7769584/working/building/REAL300000003042 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003042 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003042/0 /scratch/stefan/7769584/working/building/REAL300000003042 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/44 `/scratch/stefan/7769584/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003042 none COC(=O)C1=C(C)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 60, 76, 60, 60, 60, 60, 32, 32, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 60, 76, 76, 76, 60, 60, 60, 60, 32, 7, 1, 1, 1, 1] 76 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003042 none COC(=O)C1=C(C)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 39, 60, 60, 39, 43, 60, 60, 60, 60, 1, 12, 12, 12, 2, 2, 2, 1, 6, 39, 60, 60, 60, 60] 76 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 28] set([0, 1, 3, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003042 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003042/1 /scratch/stefan/7769584/working/building/REAL300000003042 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/45 `/scratch/stefan/7769584/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003042.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003042 none COC(=O)C1=C(C)C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 107, 168, 107, 107, 105, 107, 32, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 168, 168, 168, 107, 107, 107, 107, 32, 32, 1, 1, 1, 1] 168 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003042 none COC(=O)C1=C(C)C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 64, 64, 106, 106, 64, 66, 106, 106, 106, 106, 1, 11, 11, 11, 2, 2, 2, 1, 8, 8, 106, 106, 106, 106] 168 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 28] set([0, 1, 3, 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: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003042 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003042 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003042/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003042/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003042 Building REAL300000003043 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003043' /scratch/stefan/7769584/working/building/REAL300000003043 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003043 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003043/0 /scratch/stefan/7769584/working/building/REAL300000003043 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/46 `/scratch/stefan/7769584/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=NC=C2)C=C1) `REAL300000003043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003043 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 97, 81, 21, 21, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 81, 21, 6, 6, 1, 1, 1, 1, 97, 97] 97 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 220 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003043 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 77, 89, 89, 65, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 89, 89, 89, 89, 65, 12, 1, 1, 6, 6, 6, 6, 89, 89] 97 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003043 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 43, 43, 91, 91, 91, 91, 91, 98, 98, 94, 98, 98, 1, 1, 1, 1, 11, 43, 91, 91, 98, 98, 98, 98, 1, 1] 98 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003043 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003043/1 /scratch/stefan/7769584/working/building/REAL300000003043 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/47 `/scratch/stefan/7769584/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1) `REAL300000003043.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003043 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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 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, 25, 27, 27, 25, 13, 13, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 25, 13, 5, 5, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 84 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003043 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 22, 27, 27, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 2, 5, 5, 27, 27, 27, 27, 22, 10, 1, 1, 5, 5, 5, 5, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003043 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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 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, 10, 25, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 10, 25, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 51 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003043 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003043 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003043/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003043/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003043 Building REAL300000003044 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003044' /scratch/stefan/7769584/working/building/REAL300000003044 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003044 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003044/0 /scratch/stefan/7769584/working/building/REAL300000003044 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/48 `/scratch/stefan/7769584/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@H+](CC2=CC=CC=C2)C1) `REAL300000003044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003044 none CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@H+](CC2=CC=CC=C2)C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 11, 1, 1, 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, 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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 34, 34, 34, 34, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 1, 11, 11] 34 rigid atoms, others: [54, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56]) total number of confs: 106 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003044 none CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@H+](CC2=CC=CC=C2)C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 11, 1, 1, 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, 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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 1, 1, 1, 1, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 21, 21] 34 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 131 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: REAL300000003044 none CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@H+](CC2=CC=CC=C2)C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 11, 1, 1, 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, 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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 4, 18, 18, 21, 21, 18, 18, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 21, 21, 21, 21, 1, 1, 1, 1, 7, 7, 11, 11, 9, 11, 11, 1, 1] 34 rigid atoms, others: [1, 4, 5, 44, 45, 46, 47, 17, 18, 19, 20, 21, 55, 56, 28] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003044 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003044/1 /scratch/stefan/7769584/working/building/REAL300000003044 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/49 `/scratch/stefan/7769584/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@@H+](CC2=CC=CC=C2)C1) `REAL300000003044.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003044 none CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@@H+](CC2=CC=CC=C2)C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 11, 1, 1, 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, 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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 3, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 34, 34, 34, 34, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 1, 11, 11] 34 rigid atoms, others: [54, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56]) total number of confs: 106 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003044 none CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@@H+](CC2=CC=CC=C2)C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 11, 1, 1, 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, 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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 14, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 1, 1, 1, 1, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 21, 21] 34 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 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: REAL300000003044 none CC(C)(C)C1(CN=NC2=CC=C(C(=O)[O-])C=C2)CC[N@@H+](CC2=CC=CC=C2)C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 11, 1, 1, 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, 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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 4, 18, 18, 21, 21, 18, 18, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 11, 11, 7, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 21, 21, 21, 21, 1, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 1, 1] 34 rigid atoms, others: [1, 4, 5, 44, 45, 46, 47, 17, 18, 19, 20, 21, 55, 56, 28] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 104 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003044 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003044 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003044/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003044/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003044 Building REAL300000003045 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003045' /scratch/stefan/7769584/working/building/REAL300000003045 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003045 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003045/0 /scratch/stefan/7769584/working/building/REAL300000003045 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/50 `/scratch/stefan/7769584/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)F)N=C1) `REAL300000003045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003045 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 8, 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, 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] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 63, 107, 107, 65, 91, 107, 107, 107, 107, 1, 1, 1, 1, 1, 12, 12, 1, 1, 11, 11, 11, 63, 107, 107, 107, 107, 1, 1, 12, 1] 119 rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32]) 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: REAL300000003045 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 8, 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, 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] 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: [33, 33, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 107, 107, 107, 107, 119, 119, 107, 107, 34, 34, 34, 5, 1, 1, 1, 1, 107, 107, 119, 107] 119 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003045 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003045 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003045/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003045 Building REAL300000003046 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003046' /scratch/stefan/7769584/working/building/REAL300000003046 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003046 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003046/0 /scratch/stefan/7769584/working/building/REAL300000003046 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/51 `/scratch/stefan/7769584/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCCC2=CC=CC(OC(F)(F)F)=C2)C=C1) `REAL300000003046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003046 none O=C([O-])C1=CC=C(N=NCCC2=CC=CC(OC(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 16, 11, 16, 16, 11, 11, 3, 2, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 1, 16, 16, 16, 16, 3, 3, 2, 2, 1, 1, 1, 1, 16, 16] 22 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003046 none O=C([O-])C1=CC=C(N=NCCC2=CC=CC(OC(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 32, 55, 84, 84, 84, 84, 84, 201, 201, 201, 201, 84, 1, 1, 1, 1, 32, 32, 55, 55, 84, 84, 84, 84, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003046 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003046 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003046/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003046 Building REAL300000003047 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003047' /scratch/stefan/7769584/working/building/REAL300000003047 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003047 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003047/0 /scratch/stefan/7769584/working/building/REAL300000003047 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/52 `/scratch/stefan/7769584/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=CC=C2C1) `REAL300000003047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003047 none CC(C)(C)OC(=O)N1CCC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=CC=C2C1 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 92, 54, 92, 54, 54, 54, 54, 24, 24, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 54, 54, 54, 54, 54, 154, 154, 154, 154, 154, 154, 154, 154, 154, 54, 54, 54, 54, 24, 6, 1, 1, 1, 1, 54, 54, 54, 54, 54] 154 rigid atoms, others: [44, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52]) 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: REAL300000003047 none CC(C)(C)OC(=O)N1CCC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=CC=C2C1 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 11, 13, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 37, 54, 54, 37, 47, 54, 54, 54, 54, 1, 1, 1, 1, 1, 14, 14, 14, 13, 13, 13, 14, 14, 14, 1, 1, 1, 1, 10, 37, 54, 54, 54, 54, 1, 1, 1, 1, 1] 154 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 48, 40, 50, 51, 52, 49, 41, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003047 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003047 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003047/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003047 Building REAL300000003048 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003048' /scratch/stefan/7769584/working/building/REAL300000003048 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003048 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003048/0 /scratch/stefan/7769584/working/building/REAL300000003048 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/53 `/scratch/stefan/7769584/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2CC1(CN=NC1=CC=C(C(=O)[O-])C=C1)C2) `REAL300000003048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003048 none CC(C)(C)OC(=O)N1CC2CC1(CN=NC1=CC=C(C(=O)[O-])C=C1)C2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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, 77, 58, 77, 58, 58, 58, 58, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 84, 84, 84, 84, 84, 84, 84, 84, 84, 58, 58, 58, 58, 58, 19, 19, 1, 1, 1, 1, 58, 58] 84 rigid atoms, others: [41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003048 none CC(C)(C)OC(=O)N1CC2CC1(CN=NC1=CC=C(C(=O)[O-])C=C1)C2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [19, 18, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 48, 48, 58, 58, 48, 48, 58, 58, 58, 58, 1, 20, 20, 20, 19, 19, 19, 20, 20, 20, 1, 1, 1, 1, 1, 8, 8, 58, 58, 58, 58, 1, 1] 84 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 45, 46, 24, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003048 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003048 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003048/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003048 Building REAL300000003049 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003049' /scratch/stefan/7769584/working/building/REAL300000003049 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003049 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003049/0 /scratch/stefan/7769584/working/building/REAL300000003049 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/54 `/scratch/stefan/7769584/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C2CCCCN2C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003049 none COC(=O)C1=C2CCCCN2C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 66, 107, 66, 66, 66, 66, 66, 66, 66, 34, 34, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 66, 107, 107, 107, 66, 66, 66, 66, 66, 66, 66, 66, 34, 7, 1, 1, 1, 1, 66] 107 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) 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: REAL300000003049 none COC(=O)C1=C2CCCCN2C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 47, 66, 66, 47, 62, 66, 66, 66, 66, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 11, 47, 66, 66, 66, 66, 1] 107 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 42, 24, 28, 29, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 36, 37, 38, 39, 40, 41]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003049 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003049 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003049/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003049 Building REAL300000003050 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003050' /scratch/stefan/7769584/working/building/REAL300000003050 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003050 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003050/0 /scratch/stefan/7769584/working/building/REAL300000003050 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/55 `/scratch/stefan/7769584/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003050 none CCC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=C(C(=O)[O-])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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 4, 23, 46, 50, 50, 48, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 23, 46, 46, 50, 50, 50, 50, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 276 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: REAL300000003050 none CCC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=C(C(=O)[O-])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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 40, 40, 50, 50, 40, 41, 50, 50, 50, 50, 16, 17, 17, 16, 17, 9, 4, 4, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 12, 13, 35, 36] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 210 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003050 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003050 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003050/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003050 Building REAL300000003051 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003051' /scratch/stefan/7769584/working/building/REAL300000003051 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003051 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003051/0 /scratch/stefan/7769584/working/building/REAL300000003051 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/56 `/scratch/stefan/7769584/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCC3=CC=C(I)C=C32)C=C1) `REAL300000003051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003051 none O=C([O-])C1=CC=C(NN=C2CCC3=CC=C(I)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 18, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12] 12 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 19, 20, 21, 22, 23, 31]) total number of confs: 57 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: REAL300000003051 none O=C([O-])C1=CC=C(NN=C2CCC3=CC=C(I)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 18, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 1, 1] 12 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 25 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003051 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003051 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003051/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003051 Building REAL300000003052 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003052' /scratch/stefan/7769584/working/building/REAL300000003052 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003052 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003052/0 /scratch/stefan/7769584/working/building/REAL300000003052 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/57 `/scratch/stefan/7769584/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=C1) `REAL300000003052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003052 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=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', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 89, 89, 89, 36, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 89, 89, 89, 89, 89, 89, 90, 90, 90, 88, 36, 6, 1, 1, 1, 1, 88, 89] 90 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003052 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=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', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 12, 12, 59, 88, 88, 59, 59, 88, 88, 88, 88, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 12, 59, 88, 89, 88, 88, 1, 1] 90 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 23, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003052 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003052 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003052/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003052 Building REAL300000003053 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003053' /scratch/stefan/7769584/working/building/REAL300000003053 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003053 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003053/0 /scratch/stefan/7769584/working/building/REAL300000003053 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/58 `/scratch/stefan/7769584/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=C(Cl)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC) `REAL300000003053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003053 none C=CCOC1=C(Cl)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 94, 57, 57, 57, 57, 57, 22, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 125, 201, 201, 201, 185, 185, 57, 21, 5, 1, 1, 1, 1, 56, 125, 125, 125] 201 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) 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: REAL300000003053 none C=CCOC1=C(Cl)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 14, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 40, 56, 56, 40, 40, 56, 56, 56, 56, 1, 1, 1, 3, 53, 53, 53, 14, 14, 1, 6, 40, 56, 56, 57, 57, 1, 3, 3, 3] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 30, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003053 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003053 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003053/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003053 Building REAL300000003054 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003054' /scratch/stefan/7769584/working/building/REAL300000003054 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003054 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003054/0 /scratch/stefan/7769584/working/building/REAL300000003054 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/59 `/scratch/stefan/7769584/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(C(=O)[O-])C=C2)C=C1OC1CC1) `REAL300000003054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003054 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC1CC1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 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, 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: [69, 38, 38, 38, 38, 38, 38, 106, 106, 193, 201, 201, 199, 201, 201, 201, 201, 201, 38, 8, 1, 1, 1, 1, 69, 69, 69, 38, 38, 106, 193, 201, 201, 201, 201, 38, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 580 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003054 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC1CC1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 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, 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: [117, 67, 67, 67, 67, 21, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 164, 201, 201, 117, 117, 117, 67, 67, 20, 4, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 462 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003054 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC1CC1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 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, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 41, 66, 66, 41, 66, 66, 66, 66, 66, 1, 1, 1, 10, 38, 38, 4, 4, 4, 1, 1, 6, 41, 66, 67, 66, 66, 1, 38, 38, 38, 38, 38] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 27, 28, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 329 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003054 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003054 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003054/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003054 Building REAL300000003055 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003055' /scratch/stefan/7769584/working/building/REAL300000003055 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003055 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003055/0 /scratch/stefan/7769584/working/building/REAL300000003055 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/60 `/scratch/stefan/7769584/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C2CCCCC2=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003055 none CC(CC1=CC=C2CCCCC2=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 21, 39, 74, 74, 74, 74, 74, 74, 74, 74, 74, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 39, 39, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1] 74 rigid atoms, others: [41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 207 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003055 none CC(CC1=CC=C2CCCCC2=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 72, 72, 74, 74, 72, 74, 74, 74, 74, 74, 18, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74] 74 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003055 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003055 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003055/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003055 Building REAL300000003056 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003056' /scratch/stefan/7769584/working/building/REAL300000003056 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003056 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003056/0 /scratch/stefan/7769584/working/building/REAL300000003056 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/61 `/scratch/stefan/7769584/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2O)C=C1) `REAL300000003056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003056 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 6, 1, 1, 1, 2, 22, 22] 44 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 53 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: REAL300000003056 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 20, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 7, 19, 22, 22, 22, 44, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003056 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003056 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003056/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003056 Building REAL300000003057 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003057' /scratch/stefan/7769584/working/building/REAL300000003057 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003057 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003057/0 /scratch/stefan/7769584/working/building/REAL300000003057 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/62 `/scratch/stefan/7769584/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(F)(F)F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003057 none CN1N=C(C(F)(F)F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 27, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 27, 7, 1, 1, 1, 1] 40 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003057 none CN1N=C(C(F)(F)F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 8, 34, 40, 40, 34, 40, 40, 40, 40, 40, 2, 2, 2, 1, 8, 34, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 25] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003057 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003057 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003057/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003057 Building REAL300000003058 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003058' /scratch/stefan/7769584/working/building/REAL300000003058 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003058 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003058/0 /scratch/stefan/7769584/working/building/REAL300000003058 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/63 `/scratch/stefan/7769584/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003058 none COCC(C)OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 149, 83, 149, 16, 16, 40, 40, 16, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 201, 201, 201, 201, 201, 149, 149, 149, 149, 40, 40, 16, 4, 1, 1, 1, 1, 40, 40] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 826 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: REAL300000003058 none COCC(C)OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 18, 6, 18, 1, 1, 1, 1, 1, 1, 6, 6, 25, 40, 40, 25, 25, 40, 40, 40, 40, 1, 1, 103, 103, 103, 65, 65, 18, 18, 18, 18, 1, 1, 6, 25, 40, 40, 40, 40, 1, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 471 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003058 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003058 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003058/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003058 Building REAL300000003059 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003059' /scratch/stefan/7769584/working/building/REAL300000003059 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003059 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003059/0 /scratch/stefan/7769584/working/building/REAL300000003059 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/64 `/scratch/stefan/7769584/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)C=C1) `REAL300000003059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003059 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 197, 201, 201, 197, 129, 129, 95, 95, 95, 95, 95, 95, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 197, 129, 95, 95, 95, 95, 8, 8, 1, 1, 1, 201, 201] 201 rigid atoms, others: [38, 39, 40, 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, 41, 42]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003059 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens 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, 24, 34, 24, 34, 34, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 95, 95, 29, 95, 95, 95, 95, 34, 34, 34, 34, 24, 4, 1, 1, 1, 1, 29, 29, 95, 95, 95, 34, 34] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003059 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 21, 21, 36, 36, 36, 36, 36, 36, 74, 153, 201, 201, 153, 201, 201, 201, 201, 1, 1, 1, 1, 7, 21, 36, 36, 36, 36, 153, 153, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003059 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003059 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003059/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003059 Building REAL300000003060 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003060' /scratch/stefan/7769584/working/building/REAL300000003060 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003060 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003060/0 /scratch/stefan/7769584/working/building/REAL300000003060 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/65 `/scratch/stefan/7769584/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1) `REAL300000003060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003060 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 54, 70, 70, 54, 20, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 70, 70, 70, 70, 54, 12, 11, 11, 1, 1, 1, 11, 11, 70, 70] 70 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 250 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003060 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [26, 25, 26, 20, 26, 26, 19, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 26, 26, 26, 26, 19, 5, 1, 1, 11, 11, 11, 1, 1, 26, 26] 70 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003060 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 18, 18, 25, 25, 18, 20, 70, 70, 70, 70, 25, 25, 1, 1, 1, 1, 9, 18, 25, 25, 70, 70, 70, 25, 25, 1, 1] 70 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003060 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003060 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003060/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003060 Building REAL300000003061 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003061' /scratch/stefan/7769584/working/building/REAL300000003061 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003061 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003061/0 /scratch/stefan/7769584/working/building/REAL300000003061 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/66 `/scratch/stefan/7769584/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C([N+](=O)[O-])C=C1Br) `REAL300000003061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003061 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C([N+](=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [9, 1, 9, 9, 21, 39, 39, 29, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 21, 39, 39, 39, 39, 1, 1, 1] 39 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 133 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003061 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C([N+](=O)[O-])C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 39, 39, 39, 38, 39, 39, 39, 39, 39, 26, 26, 26, 5, 1, 1, 1, 1, 39, 39, 39] 39 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003061 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003061 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003061/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003061 Building REAL300000003062 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003062' /scratch/stefan/7769584/working/building/REAL300000003062 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003062 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003062/0 /scratch/stefan/7769584/working/building/REAL300000003062 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/67 `/scratch/stefan/7769584/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1) `REAL300000003062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003062 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 190, 200, 190, 200, 200, 190, 64, 64, 17, 17, 17, 17, 17, 5, 3, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 190, 64, 17, 17, 5, 5, 3, 3, 1, 1, 1, 1, 1, 200, 200] 201 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 569 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003062 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 102, 65, 102, 102, 64, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 11, 17, 17, 11, 17, 17, 102, 102, 102, 102, 64, 8, 1, 1, 5, 5, 11, 11, 17, 17, 17, 17, 17, 102, 102] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000003062 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2CCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 47, 47, 107, 107, 107, 107, 107, 175, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 10, 47, 107, 107, 175, 175, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003062 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003062 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003062/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003062 Building REAL300000003063 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003063' /scratch/stefan/7769584/working/building/REAL300000003063 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003063 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003063/0 /scratch/stefan/7769584/working/building/REAL300000003063 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/68 `/scratch/stefan/7769584/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2OCC(F)(F)F)C=C1) `REAL300000003063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003063 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 61, 90, 90, 55, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 90, 90, 90, 90, 55, 13, 1, 1, 1, 15, 15, 90, 90] 148 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003063 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 52, 52, 101, 101, 101, 101, 101, 101, 101, 110, 148, 148, 148, 148, 1, 1, 1, 1, 12, 52, 101, 101, 101, 148, 148, 1, 1] 148 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003063 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003063 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003063/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003063 Building REAL300000003064 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003064' /scratch/stefan/7769584/working/building/REAL300000003064 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003064 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003064/0 /scratch/stefan/7769584/working/building/REAL300000003064 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/69 `/scratch/stefan/7769584/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1) `REAL300000003064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003064 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [9, 9, 9, 9, 9, 49, 49, 128, 137, 137, 130, 137, 137, 137, 137, 137, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 49, 128, 137, 137, 137, 137, 9, 9, 9, 1, 1] 137 rigid atoms, others: [37, 38, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 375 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003064 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [88, 88, 87, 42, 41, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 137, 137, 137, 137, 88, 88, 88, 87, 41, 6, 1, 1, 1, 1, 88, 88, 88, 137, 137] 137 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 217 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: REAL300000003064 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 60, 87, 88, 64, 79, 88, 88, 88, 88, 1, 1, 1, 1, 9, 9, 9, 9, 2, 2, 2, 1, 9, 59, 87, 87, 88, 88, 2, 2, 2, 9, 9] 137 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 320 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003064 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003064/1 /scratch/stefan/7769584/working/building/REAL300000003064 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/70 `/scratch/stefan/7769584/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1) `REAL300000003064.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003064 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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: [9, 9, 9, 9, 9, 52, 146, 146, 150, 150, 146, 146, 150, 150, 150, 150, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 52, 52, 150, 150, 150, 150, 9, 9, 9, 1, 1] 150 rigid atoms, others: [37, 38, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003064 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 32, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 68, 68, 68, 68, 150, 150, 150, 150, 68, 68, 68, 68, 32, 32, 1, 1, 1, 1, 68, 68, 68, 150, 150] 150 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 281 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: REAL300000003064 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 48, 48, 68, 68, 48, 48, 68, 68, 68, 68, 1, 1, 1, 1, 9, 9, 9, 9, 2, 2, 2, 1, 9, 9, 68, 68, 68, 68, 2, 2, 2, 9, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 261 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003064 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003064 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003064/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003064/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003064 Building REAL300000003065 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003065' /scratch/stefan/7769584/working/building/REAL300000003065 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003065 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003065/0 /scratch/stefan/7769584/working/building/REAL300000003065 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/71 `/scratch/stefan/7769584/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC=C2OC(F)(F)F)C=C1) `REAL300000003065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003065 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 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] 1 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: [16, 13, 16, 12, 16, 16, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 16, 16, 16, 16, 12, 4, 2, 1, 1, 1, 16, 16] 34 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 83 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: REAL300000003065 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 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] 1 hydrogens need rotated 320 conformations in input total number of sets (complete confs): 320 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 28, 28, 104, 104, 104, 28, 104, 104, 104, 160, 160, 160, 160, 1, 1, 1, 1, 8, 28, 208, 104, 28, 104, 1, 1] 320 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 571 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003065 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003065 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003065/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003065 Building REAL300000003066 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003066' /scratch/stefan/7769584/working/building/REAL300000003066 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003066 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003066/0 /scratch/stefan/7769584/working/building/REAL300000003066 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/72 `/scratch/stefan/7769584/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(F)(F)F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003066 none CN1N=CC(C(F)(F)F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 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, 38, 38, 39, 39, 39, 24, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 23, 6, 1, 1, 1, 1] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27]) 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: REAL300000003066 none CN1N=CC(C(F)(F)F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 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, 2, 2, 2, 1, 1, 10, 10, 36, 38, 38, 36, 39, 39, 39, 39, 39, 2, 2, 2, 1, 10, 35, 38, 38, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 25] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003066 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003066 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003066/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003066 Building REAL300000003067 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003067' /scratch/stefan/7769584/working/building/REAL300000003067 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003067 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003067/0 /scratch/stefan/7769584/working/building/REAL300000003067 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/73 `/scratch/stefan/7769584/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1) `REAL300000003067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003067 none O=C([O-])C1=CC=C(N=NCC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 125, 127, 127, 125, 125, 38, 12, 12, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 127, 127, 127, 127, 38, 38, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 12, 127, 127] 127 rigid atoms, others: [37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 264 number of broken/clashed sets: 23 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003067 none O=C([O-])C1=CC=C(N=NCC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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: [87, 75, 87, 65, 87, 87, 65, 65, 10, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 10, 12, 12, 1, 1, 87, 87, 87, 87, 10, 10, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 1, 1, 1, 1, 87, 87] 127 rigid atoms, others: [32, 33, 34, 43, 9, 10, 11, 12, 13, 14, 15, 44, 22, 23, 45, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 46, 47]) total number of confs: 306 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: REAL300000003067 none O=C([O-])C1=CC=C(N=NCC2CC[NH+](CC3=CC=CC=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 34, 88, 88, 88, 88, 88, 127, 127, 127, 127, 127, 127, 88, 82, 1, 1, 1, 1, 34, 34, 88, 88, 88, 88, 88, 127, 127, 127, 127, 127, 127, 127, 88, 88, 88, 88, 1, 1] 127 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 507 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003067 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003067 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003067/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003067 Building REAL300000003068 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003068' /scratch/stefan/7769584/working/building/REAL300000003068 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003068 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003068/0 /scratch/stefan/7769584/working/building/REAL300000003068 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/74 `/scratch/stefan/7769584/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C(Br)N2)C=C1) `REAL300000003068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003068 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C(Br)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'N.pl3', 'C.ar', 'C.ar', '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, 17, 1, 17, 8, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 20, 24, 20, 24, 24, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 20, 7, 1, 1, 24, 24] 24 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 25, 26]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003068 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C(Br)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'N.pl3', 'C.ar', 'C.ar', '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, 17, 1, 17, 8, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 11, 21, 21, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 11, 21, 24, 24, 1, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003068 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003068 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003068/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003068 Building REAL300000003069 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003069' /scratch/stefan/7769584/working/building/REAL300000003069 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003069 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003069/0 /scratch/stefan/7769584/working/building/REAL300000003069 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/75 `/scratch/stefan/7769584/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1Br)NC(=O)C2=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003069 none COC1=CC2=C(C=C1Br)NC(=O)C2=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1] 14 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003069 none COC1=CC2=C(C=C1Br)NC(=O)C2=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 7, 14, 14, 14, 14, 14, 4, 4, 4, 1, 1, 1, 7, 14, 14, 14, 14] 14 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 32, 34, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003069 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003069 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003069/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003069 Building REAL300000003070 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003070' /scratch/stefan/7769584/working/building/REAL300000003070 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003070 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003070/0 /scratch/stefan/7769584/working/building/REAL300000003070 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/76 `/scratch/stefan/7769584/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC) `REAL300000003070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003070 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 62, 62, 62, 62, 62, 23, 23, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 62, 62, 143, 143, 143, 201, 201, 201, 201, 143, 143, 62, 62, 62, 62, 23, 6, 1, 1, 1, 1, 62, 62, 62, 143, 201, 201, 201] 201 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 444 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003070 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 62, 62, 43, 45, 62, 62, 62, 62, 1, 1, 6, 6, 6, 14, 14, 14, 14, 6, 6, 2, 2, 2, 1, 8, 43, 62, 62, 62, 62, 2, 2, 2, 6, 14, 14, 14] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 24, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003070 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 27, 27, 117, 143, 143, 117, 127, 143, 143, 143, 143, 6, 6, 1, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 6, 6, 27, 117, 143, 143, 143, 143, 6, 6, 6, 1, 3, 3, 3] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 47, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003070 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003070/1 /scratch/stefan/7769584/working/building/REAL300000003070 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/77 `/scratch/stefan/7769584/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC) `REAL300000003070.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003070 none COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 113, 113, 113, 113, 32, 32, 32, 32, 32, 12, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 113, 113, 113, 201, 201, 201, 201, 113, 113, 32, 32, 32, 32, 12, 12, 1, 1, 1, 1, 32, 32, 32, 113, 201, 201, 201] 201 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003070 none COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 1, 8, 8, 32, 32, 32, 32, 2, 2, 2, 5, 13, 13, 13] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 24, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) 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: REAL300000003070 none COC1=CC=C(N2C(C)=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 12, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 29, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 5, 5, 1, 1, 1, 3, 4, 4, 4, 1, 1, 5, 5, 5, 5, 29, 29, 113, 113, 113, 113, 5, 5, 5, 1, 4, 4, 4] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 47, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003070 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003070 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003070/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003070/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003070 Building REAL300000003071 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003071' /scratch/stefan/7769584/working/building/REAL300000003071 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003071 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003071/0 /scratch/stefan/7769584/working/building/REAL300000003071 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/78 `/scratch/stefan/7769584/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C2OCCCC2=C1) `REAL300000003071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003071 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C2OCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 39, 55, 55, 39, 39, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 39, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1] 55 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 243 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003071 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C2OCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 55, 55, 55, 55, 55, 55, 55, 55, 55, 33, 33, 33, 6, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003071 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003071 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003071/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003071 Building REAL300000003072 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003072' /scratch/stefan/7769584/working/building/REAL300000003072 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003072 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003072/0 /scratch/stefan/7769584/working/building/REAL300000003072 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/79 `/scratch/stefan/7769584/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C=NNC2=CC=C(C(=O)[O-])C=C2)=CN=C1Br) `REAL300000003072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003072 none CN1C(C=NNC2=CC=C(C(=O)[O-])C=C2)=CN=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 24, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 35, 35, 35, 35, 35, 35, 35, 24, 7, 1, 1, 1, 1, 35] 35 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28]) 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: REAL300000003072 none CN1C(C=NNC2=CC=C(C(=O)[O-])C=C2)=CN=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 31, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 2, 2, 2, 11, 31, 35, 35, 35, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003072 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003072 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003072/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003072 Building REAL300000003073 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003073' /scratch/stefan/7769584/working/building/REAL300000003073 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003073 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003073/0 /scratch/stefan/7769584/working/building/REAL300000003073 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/80 `/scratch/stefan/7769584/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)NC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC1) `REAL300000003073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003073 none CCOC(=O)NC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 80, 60, 80, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 86, 86, 86, 86, 86, 60, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 24, 24, 24, 24] 86 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003073 none CCOC(=O)NC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 26, 13, 7, 13, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 8, 8, 24, 23, 24, 24, 1, 1, 52, 52, 52, 52, 52, 7, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 1, 1, 1, 1] 86 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 39, 40, 42, 21, 22, 41, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003073 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003073 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003073/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003073 Building REAL300000003074 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003074' /scratch/stefan/7769584/working/building/REAL300000003074 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003074 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003074/0 /scratch/stefan/7769584/working/building/REAL300000003074 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/81 `/scratch/stefan/7769584/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN(C(=O)OC(C)(C)C)C1) `REAL300000003074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003074 none COC(=O)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 5, 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, 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: [39, 39, 15, 39, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 32, 32, 46, 46, 46, 46, 15, 39, 39, 39, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 46, 46, 46, 46, 46, 46, 46, 46, 46, 15, 15] 122 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 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: REAL300000003074 none COC(=O)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 8, 8, 15, 15, 8, 8, 15, 15, 15, 15, 1, 1, 1, 6, 6, 15, 16, 16, 16, 1, 4, 4, 4, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 122 rigid atoms, others: [32, 33, 2, 50, 4, 5, 6, 7, 40, 39, 34, 18, 19, 20, 27, 51, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003074 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003074 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003074/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003074 Building REAL300000003075 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003075' /scratch/stefan/7769584/working/building/REAL300000003075 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003075 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003075/0 /scratch/stefan/7769584/working/building/REAL300000003075 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/82 `/scratch/stefan/7769584/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C(Cl)=C1) `REAL300000003075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003075 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 16, 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, 2, 2, 7, 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: [11, 1, 11, 11, 45, 55, 55, 45, 45, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 45, 55, 55, 55, 55, 1, 1, 1] 55 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000003075 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 16, 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, 2, 2, 7, 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: [29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 55, 55, 54, 54, 55, 55, 55, 30, 30, 30, 5, 1, 1, 1, 1, 55, 55, 55] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003075 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003075 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003075/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003075 Building REAL300000003076 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003076' /scratch/stefan/7769584/working/building/REAL300000003076 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003076 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003076/0 /scratch/stefan/7769584/working/building/REAL300000003076 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/83 `/scratch/stefan/7769584/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCC2CC2=CC=CC=N2)C=C1) `REAL300000003076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003076 none O=C([O-])C1=CC=C(N=NC2CCCC2CC2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 1, 1, 1, 1, 31, 31] 31 rigid atoms, others: [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, 34, 39, 40]) total number of confs: 65 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003076 none O=C([O-])C1=CC=C(N=NC2CCCC2CC2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 10, 14, 8, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 14, 14] 31 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003076 none O=C([O-])C1=CC=C(N=NC2CCCC2CC2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 23, 31, 31, 31, 31, 31, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003076 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003076 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003076/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003076 Building REAL300000003077 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003077' /scratch/stefan/7769584/working/building/REAL300000003077 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003077 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003077/0 /scratch/stefan/7769584/working/building/REAL300000003077 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/84 `/scratch/stefan/7769584/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2CCCC(C(F)(F)F)C2)C=C1) `REAL300000003077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003077 none O=C([O-])C1=CC=C(N=NCC2CCCC(C(F)(F)F)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 34, 34, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 34 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 37, 36]) 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: REAL300000003077 none O=C([O-])C1=CC=C(N=NCC2CCCC(C(F)(F)F)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 5, 5, 19, 33, 34, 34, 34, 33, 34, 34, 34, 33, 1, 1, 1, 1, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 36, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003077 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003077 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003077/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003077 Building REAL300000003078 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003078' /scratch/stefan/7769584/working/building/REAL300000003078 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003078 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003078/0 /scratch/stefan/7769584/working/building/REAL300000003078 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/85 `/scratch/stefan/7769584/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(C)(C)CC(C)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003078 none COC(=O)CC(C)(C)CC(C)N=NC1=CC=C(C(=O)[O-])C=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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 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, 92, 129, 64, 31, 64, 64, 23, 4, 23, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 92, 92, 64, 64, 64, 64, 64, 64, 31, 31, 23, 23, 23, 23, 1, 1, 1, 1] 129 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 561 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003078 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003078 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003078/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003078 Building REAL300000003079 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003079' /scratch/stefan/7769584/working/building/REAL300000003079 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003079 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003079/0 /scratch/stefan/7769584/working/building/REAL300000003079 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/86 `/scratch/stefan/7769584/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(C(F)(F)F)N=C3CCCCN32)C=C1) `REAL300000003079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003079 none O=C([O-])C1=CC=C(NN=CC2=C(C(F)(F)F)N=C3CCCCN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 8, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 31 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 13, 14, 15, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003079 none O=C([O-])C1=CC=C(NN=CC2=C(C(F)(F)F)N=C3CCCCN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 24, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003079 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003079 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003079/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003079 Building REAL300000003080 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003080' /scratch/stefan/7769584/working/building/REAL300000003080 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003080 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003080/0 /scratch/stefan/7769584/working/building/REAL300000003080 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/87 `/scratch/stefan/7769584/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=C1Br) `REAL300000003080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003080 none CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 17, 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, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 10] 11 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003080 none CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 17, 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, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 10, 10, 10, 10, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 17, 18, 19, 20, 21, 22, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003080 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003080 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003080/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003080 Building REAL300000003081 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003081' /scratch/stefan/7769584/working/building/REAL300000003081 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003081 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003081/0 /scratch/stefan/7769584/working/building/REAL300000003081 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/88 `/scratch/stefan/7769584/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)C=C1) `REAL300000003081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003081 none O=C([O-])C1=CC=C(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 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: [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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [41, 32, 41, 29, 41, 41, 29, 29, 7, 1, 7, 18, 24, 24, 18, 21, 24, 24, 1, 1, 1, 1, 41, 41, 41, 41, 7, 18, 18, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 41, 41] 51 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003081 none O=C([O-])C1=CC=C(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 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: [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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 41, 35, 41, 41, 35, 35, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 41, 41, 41, 41, 9, 3, 3, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 41, 41] 51 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000003081 none O=C([O-])C1=CC=C(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 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: [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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 40, 41, 41, 40, 41, 41, 41, 24, 42, 42, 42, 1, 1, 1, 1, 24, 40, 40, 41, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 1, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003081 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003081 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003081/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003081 Building REAL300000003082 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003082' /scratch/stefan/7769584/working/building/REAL300000003082 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003082 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003082/0 /scratch/stefan/7769584/working/building/REAL300000003082 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/89 `/scratch/stefan/7769584/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(C)C) `REAL300000003082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003082 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(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', 'C.2', 'O.co2', 'O.co2', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 38, 39, 39, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 21, 5, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 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: REAL300000003082 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(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', 'C.2', 'O.co2', 'O.co2', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 31, 39, 39, 31, 31, 39, 39, 39, 39, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 11, 31, 39, 39, 39, 39, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 26, 27, 28, 35] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003082 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003082 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003082/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003082 Building REAL300000003083 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003083' /scratch/stefan/7769584/working/building/REAL300000003083 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003083 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003083/0 /scratch/stefan/7769584/working/building/REAL300000003083 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/90 `/scratch/stefan/7769584/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(CC3CCC3)=C2)C=C1) `REAL300000003083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003083 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(CC3CCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 201, 166, 201, 201, 166, 67, 67, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 166, 67, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 17, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) total number of confs: 659 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003083 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(CC3CCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 50, 72, 50, 72, 72, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 1, 72, 72, 72, 72, 50, 10, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 17, 17, 1, 73, 73] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) 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: REAL300000003083 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(CC3CCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 32, 33, 73, 73, 33, 73, 73, 128, 201, 201, 201, 73, 1, 1, 1, 1, 11, 32, 73, 73, 33, 128, 128, 201, 201, 201, 201, 201, 201, 201, 73, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003083 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003083 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003083/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003083 Building REAL300000003084 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003084' /scratch/stefan/7769584/working/building/REAL300000003084 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003084 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003084/0 /scratch/stefan/7769584/working/building/REAL300000003084 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/91 `/scratch/stefan/7769584/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003084 none CCOC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 92, 88, 37, 88, 37, 37, 37, 37, 26, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 99, 99, 99, 99, 99, 37, 37, 37, 25, 5, 1, 1, 1, 1] 99 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003084 none CCOC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [32, 20, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 17, 37, 37, 20, 20, 37, 37, 37, 37, 1, 32, 32, 32, 32, 32, 1, 1, 1, 4, 17, 37, 37, 37, 37] 99 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003084 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003084/1 /scratch/stefan/7769584/working/building/REAL300000003084 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/92 `/scratch/stefan/7769584/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003084.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003084 none CCOC(=O)C1=CC=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 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, 195, 183, 78, 183, 78, 78, 78, 78, 25, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 78, 201, 201, 201, 201, 201, 78, 78, 78, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000003084 none CCOC(=O)C1=CC=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 24, 12, 1, 12, 1, 1, 1, 1, 1, 1, 8, 52, 52, 78, 78, 60, 78, 78, 78, 78, 78, 1, 46, 46, 46, 46, 46, 1, 1, 1, 8, 8, 78, 78, 78, 78] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003084 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003084 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003084/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003084/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003084 Building REAL300000003085 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003085' /scratch/stefan/7769584/working/building/REAL300000003085 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003085 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003085/0 /scratch/stefan/7769584/working/building/REAL300000003085 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/93 `/scratch/stefan/7769584/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(F)=C(Cl)C=C23)C=C1) `REAL300000003085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003085 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(F)=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 41, 11, 1, 1, 1, 1, 54, 54] 54 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003085 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(F)=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 39, 39, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 9, 39, 54, 54, 54, 54, 1, 1] 54 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003085 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003085/1 /scratch/stefan/7769584/working/building/REAL300000003085 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/94 `/scratch/stefan/7769584/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(F)=C(Cl)C=C23)C=C1) `REAL300000003085.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003085 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(F)=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 9, 9, 1, 1, 1, 1, 44, 44] 44 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003085 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(F)=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 15, 15, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003085 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003085 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003085/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003085/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003085 Building REAL300000003086 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003086' /scratch/stefan/7769584/working/building/REAL300000003086 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003086 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003086/0 /scratch/stefan/7769584/working/building/REAL300000003086 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/95 `/scratch/stefan/7769584/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(I)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003086 none CN1N=CC(I)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 18, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 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, 27, 27, 27, 27, 27, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 20, 6, 1, 1, 1, 1] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24]) 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: REAL300000003086 none CN1N=CC(I)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 18, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 27, 27, 22, 22, 27, 27, 27, 27, 2, 2, 2, 1, 10, 22, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003086 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003086 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003086/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003086 Building REAL300000003087 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003087' /scratch/stefan/7769584/working/building/REAL300000003087 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003087 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003087/0 /scratch/stefan/7769584/working/building/REAL300000003087 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/96 `/scratch/stefan/7769584/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(OC(F)(F)F)C=C32)C=C1) `REAL300000003087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003087 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(OC(F)(F)F)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 24, 24, 24, 1, 1, 27, 27, 27, 27, 7, 1, 1, 1, 1, 27, 27] 66 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 18, 19, 20, 21, 24, 25, 26, 27, 28]) 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: REAL300000003087 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(OC(F)(F)F)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 65, 65, 65, 65, 29, 29, 1, 1, 1, 1, 9, 29, 29, 29, 29, 1, 1] 65 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003087 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003087 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003087/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003087 Building REAL300000003088 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003088' /scratch/stefan/7769584/working/building/REAL300000003088 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003088 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003088/0 /scratch/stefan/7769584/working/building/REAL300000003088 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/97 `/scratch/stefan/7769584/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(F)C(Br)=C32)C=C1) `REAL300000003088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003088 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(F)C(Br)=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 7, 1, 1, 1, 11, 11] 11 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003088 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(F)C(Br)=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003088 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003088 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003088/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003088 Building REAL300000003089 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003089' /scratch/stefan/7769584/working/building/REAL300000003089 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003089 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003089/0 /scratch/stefan/7769584/working/building/REAL300000003089 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/98 `/scratch/stefan/7769584/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O) `REAL300000003089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003089 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Cl)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 1 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: [52, 52, 52, 52, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 32, 6, 1, 1, 1, 1, 52, 104] 104 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003089 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Cl)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 1 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, 1, 1, 1, 1, 10, 10, 44, 52, 52, 45, 44, 52, 52, 52, 52, 1, 1, 1, 1, 1, 4, 4, 4, 1, 10, 44, 52, 52, 52, 52, 1, 2] 104 rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003089 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003089 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003089/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003089 Building REAL300000003090 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003090' /scratch/stefan/7769584/working/building/REAL300000003090 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003090 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003090/0 /scratch/stefan/7769584/working/building/REAL300000003090 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/99 `/scratch/stefan/7769584/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(Cl)N=CC=C3S2)C=C1) `REAL300000003090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003090 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Cl)N=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 38, 41, 41, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 41, 34, 10, 1, 1, 1, 40, 40] 41 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003090 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Cl)N=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 29, 30, 40, 41, 41, 40, 41, 41, 41, 41, 41, 1, 1, 1, 1, 9, 29, 40, 41, 41, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003090 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003090 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003090/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003090 Building REAL300000003091 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003091' /scratch/stefan/7769584/working/building/REAL300000003091 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003091 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003091/0 /scratch/stefan/7769584/working/building/REAL300000003091 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/100 `/scratch/stefan/7769584/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC=NC(Cl)=C3S2)C=C1) `REAL300000003091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003091 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=NC(Cl)=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 29, 32, 32, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 32, 32, 32, 28, 6, 1, 1, 1, 31, 32] 32 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003091 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=NC(Cl)=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 10, 25, 32, 32, 32, 1, 1] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003091 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003091 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003091/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003091 Building REAL300000003092 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003092' /scratch/stefan/7769584/working/building/REAL300000003092 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003092 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003092/0 /scratch/stefan/7769584/working/building/REAL300000003092 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/101 `/scratch/stefan/7769584/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(C)CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(C)C) `REAL300000003092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003092 none COC1=CC=C(CC(C)CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(C)C 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', 'C.2', 'O.co2', 'O.co2', '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', '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, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 141, 201, 201, 141, 87, 31, 85, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 140, 93, 93, 93, 93, 31, 31, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1006 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003092 none COC1=CC=C(CC(C)CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C(C)(C)C 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', 'C.2', 'O.co2', 'O.co2', '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', '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, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 71, 200, 200, 201, 201, 200, 200, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 6, 15, 15, 15, 15, 69, 69, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 21, 22, 23, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003092 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003092 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003092/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003092 Building REAL300000003093 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003093' /scratch/stefan/7769584/working/building/REAL300000003093 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003093 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003093/0 /scratch/stefan/7769584/working/building/REAL300000003093 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/102 `/scratch/stefan/7769584/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2(C3CCCCO3)CCC2)C=C1) `REAL300000003093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003093 none O=C([O-])C1=CC=C(N=NCC2(C3CCCCO3)CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 22, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 51, 51, 51, 51, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 51, 51] 51 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003093 none O=C([O-])C1=CC=C(N=NCC2(C3CCCCO3)CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [38, 35, 38, 35, 38, 38, 35, 35, 10, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 38, 38, 38, 38, 10, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 38, 38] 51 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42]) total number of confs: 105 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: REAL300000003093 none O=C([O-])C1=CC=C(N=NCC2(C3CCCCO3)CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 4, 4, 23, 43, 52, 52, 52, 52, 52, 43, 43, 43, 1, 1, 1, 1, 23, 23, 52, 52, 52, 52, 52, 52, 52, 52, 52, 43, 43, 43, 43, 43, 43, 1, 1] 52 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 20, 21, 22, 23] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003093 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003093 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003093/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003093 Building REAL300000003094 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003094' /scratch/stefan/7769584/working/building/REAL300000003094 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003094 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003094/0 /scratch/stefan/7769584/working/building/REAL300000003094 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/103 `/scratch/stefan/7769584/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC(C)=CC=C21) `REAL300000003094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003094 none CCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC(C)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 33, 32, 32, 33, 32, 32, 32, 6, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19] 33 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003094 none CCCN1C(=O)C(=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC(C)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 7, 7, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 4, 4, 7, 19, 19, 18, 18, 1, 2, 2, 2, 1, 1] 33 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 41, 42, 18, 19, 20, 21, 22, 23, 24, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003094 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003094 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003094/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003094 Building REAL300000003095 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003095' /scratch/stefan/7769584/working/building/REAL300000003095 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003095 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003095/0 /scratch/stefan/7769584/working/building/REAL300000003095 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/104 `/scratch/stefan/7769584/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC(F)(F)F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003095 none COC1=CC=CC(OC(F)(F)F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 104, 104, 104, 20, 104, 104, 104, 187, 201, 201, 201, 20, 20, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 135, 135, 135, 104, 20, 104, 20, 6, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003095 none COC1=CC=CC(OC(F)(F)F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 18, 18, 18, 1, 1, 12, 12, 69, 104, 104, 70, 70, 104, 104, 104, 104, 3, 3, 3, 1, 1, 1, 12, 69, 104, 104, 104, 104] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 12, 13, 28, 29, 30] set([0, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003095 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003095/1 /scratch/stefan/7769584/working/building/REAL300000003095 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/105 `/scratch/stefan/7769584/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC(F)(F)F)=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003095.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003095 none COC1=CC=CC(OC(F)(F)F)=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 26, 26, 24, 26, 26, 26, 26, 30, 30, 30, 17, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 30, 26, 26, 26, 17, 17, 1, 1, 1, 1] 30 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000003095 none COC1=CC=CC(OC(F)(F)F)=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 1, 1, 5, 21, 21, 26, 26, 21, 21, 26, 26, 26, 26, 3, 3, 3, 1, 1, 1, 5, 5, 26, 26, 26, 26] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 12, 13, 28, 29, 30] set([0, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003095 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003095 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003095/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003095/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003095 Building REAL300000003096 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003096' /scratch/stefan/7769584/working/building/REAL300000003096 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003096 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003096/0 /scratch/stefan/7769584/working/building/REAL300000003096 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/106 `/scratch/stefan/7769584/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(OC3=CC=C(F)C=C3)N=C3C=CC=CN32)C=C1) `REAL300000003096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003096 none O=C([O-])C1=CC=C(NN=CC2=C(OC3=CC=C(F)C=C3)N=C3C=CC=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 166, 184, 166, 184, 184, 166, 64, 64, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 184, 184, 184, 184, 166, 64, 1, 1, 1, 1, 20, 20, 20, 20, 184, 184] 184 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 554 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003096 none O=C([O-])C1=CC=C(NN=CC2=C(OC3=CC=C(F)C=C3)N=C3C=CC=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [68, 52, 68, 52, 68, 68, 51, 10, 10, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 51, 10, 20, 20, 20, 20, 1, 1, 1, 1, 68, 68] 184 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) 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: REAL300000003096 none O=C([O-])C1=CC=C(NN=CC2=C(OC3=CC=C(F)C=C3)N=C3C=CC=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 35, 35, 70, 70, 157, 185, 185, 185, 185, 185, 185, 70, 70, 70, 71, 71, 70, 70, 1, 1, 1, 1, 9, 35, 185, 185, 185, 185, 70, 71, 71, 70, 1, 1] 185 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003096 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003096 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003096/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003096 Building REAL300000003097 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003097' /scratch/stefan/7769584/working/building/REAL300000003097 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003097 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003097/0 /scratch/stefan/7769584/working/building/REAL300000003097 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/107 `/scratch/stefan/7769584/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCCC2=CC=CC(C(F)(F)F)=C2)C=C1) `REAL300000003097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003097 none O=C([O-])C1=CC=C(N=NCCC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 56, 56, 56, 13, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 56, 56, 56, 56, 13, 13, 9, 9, 1, 1, 1, 1, 56, 56] 56 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000003097 none O=C([O-])C1=CC=C(N=NCCC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 21, 34, 56, 56, 51, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 21, 21, 34, 34, 56, 56, 51, 56, 1, 1] 56 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003097 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003097 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003097/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003097 Building REAL300000003098 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003098' /scratch/stefan/7769584/working/building/REAL300000003098 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003098 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003098/0 /scratch/stefan/7769584/working/building/REAL300000003098 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/108 `/scratch/stefan/7769584/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=NC=C1Br) `REAL300000003098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003098 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=NC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 15, 5, 1, 1, 1, 1, 19] 19 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) 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: REAL300000003098 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=NC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 15, 19, 19, 15, 15, 19, 19, 19, 19, 1, 1, 1, 1, 2, 2, 2, 1, 7, 15, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 23, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003098 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003098/1 /scratch/stefan/7769584/working/building/REAL300000003098 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/109 `/scratch/stefan/7769584/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=NC=C1Br) `REAL300000003098.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003098 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=NC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 7, 7, 7, 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, 3, 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, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 13, 13, 1, 1, 1, 1, 45] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) 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: REAL300000003098 none CC1=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=NC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 7, 7, 7, 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, 3, 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, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 2, 2, 2, 1, 9, 9, 45, 45, 45, 45, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 23, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003098 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003098 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003098/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003098/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003098 Building REAL300000003099 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003099' /scratch/stefan/7769584/working/building/REAL300000003099 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003099 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003099/0 /scratch/stefan/7769584/working/building/REAL300000003099 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/110 `/scratch/stefan/7769584/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1F) `REAL300000003099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003099 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 20, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 22, 28, 28, 28, 28, 28, 19, 6, 1, 1, 1, 1, 28] 28 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003099 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 24, 28, 28, 24, 24, 28, 28, 28, 28, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 24, 28, 28, 28, 28, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 24, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003099 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003099 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003099/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003099 Building REAL300000003100 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003100' /scratch/stefan/7769584/working/building/REAL300000003100 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003100 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003100/0 /scratch/stefan/7769584/working/building/REAL300000003100 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/111 `/scratch/stefan/7769584/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(C)(CN=NC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000003100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003100 none CC(C)(C)OC(=O)N1CCCC(C)(CN=NC2=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 151, 102, 151, 102, 102, 102, 98, 23, 102, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 173, 173, 173, 173, 173, 173, 173, 173, 173, 102, 102, 102, 102, 101, 101, 102, 102, 102, 23, 23, 1, 1, 1, 1, 102, 102] 173 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003100 none CC(C)(C)OC(=O)N1CCCC(C)(CN=NC2=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [22, 21, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 9, 63, 63, 101, 101, 63, 63, 101, 101, 101, 101, 1, 23, 23, 23, 22, 22, 22, 23, 23, 23, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 101, 101, 101, 101, 1, 1] 173 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 40, 50, 51, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003100 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003100 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003100/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003100 Building REAL300000003101 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003101' /scratch/stefan/7769584/working/building/REAL300000003101 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003101 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003101/0 /scratch/stefan/7769584/working/building/REAL300000003101 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/112 `/scratch/stefan/7769584/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2CCC(N=NC3=CC=C(C(=O)[O-])C=C3)C21) `REAL300000003101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003101 none CC(C)(C)OC(=O)N1CCC2CCC(N=NC3=CC=C(C(=O)[O-])C=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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 22, 13, 22, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13] 23 rigid atoms, others: [48, 45, 46, 15, 16, 17, 18, 19, 20, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49]) total number of confs: 66 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003101 none CC(C)(C)OC(=O)N1CCC2CCC(N=NC3=CC=C(C(=O)[O-])C=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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [16, 12, 16, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 7, 8, 13, 13, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1] 23 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 40, 43, 41, 25, 49, 42, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003101 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003101 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003101/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003101 Building REAL300000003102 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003102' /scratch/stefan/7769584/working/building/REAL300000003102 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003102 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003102/0 /scratch/stefan/7769584/working/building/REAL300000003102 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/113 `/scratch/stefan/7769584/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003102 none CC(C)(C)OC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 122, 68, 122, 68, 68, 68, 35, 35, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 68, 164, 164, 164, 164, 164, 164, 164, 164, 164, 68, 68, 35, 7, 1, 1, 1, 1] 164 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300000003102 none CC(C)(C)OC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 26, 33, 32, 12, 1, 12, 1, 1, 1, 1, 1, 10, 10, 49, 68, 68, 49, 49, 68, 68, 68, 68, 1, 33, 33, 33, 33, 32, 33, 33, 33, 33, 1, 1, 10, 48, 68, 68, 68, 68] 164 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23] set([0, 1, 2, 3, 4, 6, 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]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003102 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003102 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003102/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003102 Building REAL300000003103 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003103' /scratch/stefan/7769584/working/building/REAL300000003103 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003103 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003103/0 /scratch/stefan/7769584/working/building/REAL300000003103 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/114 `/scratch/stefan/7769584/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)OC(C)(C)C)CC1N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003103 none CC1CN(C(=O)OC(C)(C)C)CC1N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [20, 20, 20, 20, 20, 34, 34, 53, 56, 56, 56, 20, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 56, 56, 56, 56, 56, 56, 56, 56, 56, 20, 20, 20, 1, 1, 1, 1] 56 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000003103 none CC1CN(C(=O)OC(C)(C)C)CC1N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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, 6, 6, 15, 18, 18, 18, 1, 1, 1, 13, 13, 20, 20, 13, 13, 20, 19, 20, 20, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 20, 20, 20, 20] 56 rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 41, 11, 12, 13, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003103 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003103 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003103/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003103 Building REAL300000003104 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003104' /scratch/stefan/7769584/working/building/REAL300000003104 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003104 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003104/0 /scratch/stefan/7769584/working/building/REAL300000003104 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/115 `/scratch/stefan/7769584/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC=C2Br)C=C1) `REAL300000003104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003104 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 38, 49, 38, 49, 49, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 38, 12, 2, 1, 1, 1, 49, 49] 98 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 190 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003104 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 30, 30, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 11, 30, 98, 49, 49, 49, 1, 1] 98 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003104 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003104 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003104/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003104 Building REAL300000003105 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003105' /scratch/stefan/7769584/working/building/REAL300000003105 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003105 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003105/0 /scratch/stefan/7769584/working/building/REAL300000003105 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/116 `/scratch/stefan/7769584/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(SC(F)(F)F)=C1) `REAL300000003105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003105 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(SC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 27, 55, 55, 27, 32, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 10, 19, 19, 19, 1, 8, 8, 8, 27, 55, 55, 55, 55, 1, 1, 1, 1] 73 rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300000003105 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(SC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 55, 55, 55, 55, 55, 73, 73, 73, 73, 55, 28, 28, 28, 5, 1, 1, 1, 1, 55, 55, 55, 55] 73 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003105 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003105 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003105/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003105 Building REAL300000003106 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003106' /scratch/stefan/7769584/working/building/REAL300000003106 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003106 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003106/0 /scratch/stefan/7769584/working/building/REAL300000003106 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/117 `/scratch/stefan/7769584/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1Br) `REAL300000003106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003106 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 15, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 25, 25, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 25, 7, 1, 1, 1, 1, 36] 36 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003106 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 15, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 27, 36, 36, 34, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 3, 1, 8, 27, 36, 36, 36, 36, 1] 36 rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003106 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003106 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003106/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003106 Building REAL300000003107 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003107' /scratch/stefan/7769584/working/building/REAL300000003107 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003107 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003107/0 /scratch/stefan/7769584/working/building/REAL300000003107 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/118 `/scratch/stefan/7769584/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(Br)=C2Cl)C=C1) `REAL300000003107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003107 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Br)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 27, 23, 27, 27, 23, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 23, 10, 1, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 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: REAL300000003107 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Br)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 23, 23, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 11, 23, 27, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003107 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003107 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003107/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003107 Building REAL300000003108 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003108' /scratch/stefan/7769584/working/building/REAL300000003108 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003108 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003108/0 /scratch/stefan/7769584/working/building/REAL300000003108 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/119 `/scratch/stefan/7769584/working/3D/119' -> `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(C(=O)[O-])C=C2)N=N1) `REAL300000003108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003108 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 8, 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, 2, 2, 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 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, 46, 38, 46, 32, 32, 32, 32, 27, 27, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 60, 60, 60, 60, 60, 60, 60, 60, 60, 38, 32, 32, 27, 6, 1, 1, 1, 1] 60 rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000003108 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 8, 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, 2, 2, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 14, 14, 9, 6, 9, 1, 1, 1, 1, 1, 1, 4, 4, 16, 32, 32, 22, 32, 32, 32, 32, 32, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 4, 16, 32, 32, 32, 32] 60 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 24, 25] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003108 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003108/1 /scratch/stefan/7769584/working/building/REAL300000003108 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/120 `/scratch/stefan/7769584/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=N1) `REAL300000003108.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003108 none CC(C)(C)OC(=O)NC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 150, 119, 150, 58, 58, 58, 58, 19, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 58, 58, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003108 none CC(C)(C)OC(=O)NC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 23, 23, 13, 8, 13, 1, 1, 1, 1, 1, 1, 9, 47, 47, 58, 58, 47, 47, 58, 58, 58, 58, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 1, 1, 9, 9, 58, 58, 58, 58] 201 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 24, 25] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003108 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003108 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003108/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003108/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003108 Building REAL300000003109 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003109' /scratch/stefan/7769584/working/building/REAL300000003109 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003109 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003109/0 /scratch/stefan/7769584/working/building/REAL300000003109 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/121 `/scratch/stefan/7769584/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(CNC(=O)OC(C)(C)C)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003109 none CCOCC(CNC(=O)OC(C)(C)C)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', '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, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 58, 30, 17, 4, 17, 25, 96, 140, 140, 171, 172, 172, 172, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 59, 59, 59, 59, 30, 30, 17, 25, 25, 96, 172, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1, 1, 1] 201 rigid atoms, others: [48, 45, 46, 15, 16, 17, 18, 19, 20, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003109 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003109 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003109/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003109 Building REAL300000003110 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003110' /scratch/stefan/7769584/working/building/REAL300000003110 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003110 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003110/0 /scratch/stefan/7769584/working/building/REAL300000003110 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/122 `/scratch/stefan/7769584/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003110 none CCC(C)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 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, 113, 78, 113, 62, 112, 112, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 112, 112, 114, 114, 114, 114, 114, 113, 113, 111, 113, 112, 112, 34, 34, 34, 6, 1, 1, 1, 1, 112, 112] 114 rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 498 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: REAL300000003110 none CCC(C)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 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: [7, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 12, 66, 112, 112, 66, 94, 112, 112, 112, 112, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 1, 1, 13, 13, 13, 66, 112, 112, 112, 112, 1, 1] 114 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 42, 43, 21, 22] set([0, 1, 3, 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, 39, 40, 41]) total number of confs: 490 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003110 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003110 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003110/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003110 Building REAL300000003111 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003111' /scratch/stefan/7769584/working/building/REAL300000003111 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003111 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003111/0 /scratch/stefan/7769584/working/building/REAL300000003111 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/123 `/scratch/stefan/7769584/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)SC(C)=C1) `REAL300000003111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003111 none CCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)SC(C)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 41, 9, 1, 9, 9, 63, 135, 135, 80, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 41, 41, 63, 135, 135, 135, 135, 2, 2, 2, 2, 2, 2, 1] 162 rigid atoms, others: [3, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 733 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: REAL300000003111 none CCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)SC(C)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [121, 102, 37, 37, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 135, 135, 135, 135, 135, 135, 123, 123, 123, 123, 123, 102, 102, 7, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135] 162 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 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: 570 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003111 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003111 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003111/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003111 Building REAL300000003112 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003112' /scratch/stefan/7769584/working/building/REAL300000003112 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003112 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003112/0 /scratch/stefan/7769584/working/building/REAL300000003112 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/124 `/scratch/stefan/7769584/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1) `REAL300000003112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003112 none CN1C=C(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 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, 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: [72, 72, 72, 56, 56, 56, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 56, 56, 72, 72, 72, 72, 72, 72, 40, 7, 1, 1, 1, 1, 56, 72] 72 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003112 none CN1C=C(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 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, 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, 4, 4, 1, 1, 1, 1, 1, 7, 7, 38, 56, 56, 44, 56, 56, 56, 56, 56, 1, 1, 4, 4, 5, 5, 5, 5, 7, 38, 56, 56, 56, 56, 1, 5] 72 rigid atoms, others: [33, 3, 4, 5, 6, 7, 19, 20] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) 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: REAL300000003112 none CN1C=C(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 5, 20, 20, 52, 72, 72, 72, 72, 72, 72, 72, 72, 4, 5, 1, 1, 2, 2, 2, 1, 20, 52, 72, 72, 72, 72, 4, 1] 72 rigid atoms, others: [0, 1, 2, 3, 4, 34, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003112 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003112 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003112/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003112 Building REAL300000003113 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003113' /scratch/stefan/7769584/working/building/REAL300000003113 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003113 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003113/0 /scratch/stefan/7769584/working/building/REAL300000003113 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/125 `/scratch/stefan/7769584/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1Cl) `REAL300000003113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003113 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 35, 6, 1, 1, 1, 1, 69, 69] 69 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003113 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 48, 69, 69, 62, 69, 69, 69, 69, 69, 1, 1, 1, 1, 4, 4, 4, 1, 10, 48, 69, 69, 69, 69, 1, 1] 69 rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 24, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003113 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003113 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003113/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003113 Building REAL300000003114 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003114' /scratch/stefan/7769584/working/building/REAL300000003114 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003114 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003114/0 /scratch/stefan/7769584/working/building/REAL300000003114 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/126 `/scratch/stefan/7769584/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1OCCCC2=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003114 none COC1=CC=CC2=C1OCCCC2=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 24, 24, 24, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1] 25 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003114 none COC1=CC=CC2=C1OCCCC2=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 8, 8, 24, 24, 24, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 25, 24, 24] 25 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003114 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003114/1 /scratch/stefan/7769584/working/building/REAL300000003114 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/127 `/scratch/stefan/7769584/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1OCCCC2N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003114.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003114 none COC1=CC=CC2=C1OCCCC2N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003114 none COC1=CC=CC2=C1OCCCC2N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 7, 7, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 9 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, 36] set([0, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003114 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003114 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003114/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003114/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003114 Building REAL300000003115 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003115' /scratch/stefan/7769584/working/building/REAL300000003115 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003115 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003115/0 /scratch/stefan/7769584/working/building/REAL300000003115 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/128 `/scratch/stefan/7769584/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1) `REAL300000003115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003115 none O=C([O-])C1=CC=C(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 51, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 52, 52, 52, 52, 14, 14, 4, 1, 1, 1, 1, 52, 52] 52 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 92 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003115 none O=C([O-])C1=CC=C(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 52, 52, 45, 45, 9, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 4, 1, 1, 52, 52, 52, 52, 9, 9, 1, 4, 4, 4, 4, 52, 52] 52 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) 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: REAL300000003115 none O=C([O-])C1=CC=C(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 5, 5, 23, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 23, 23, 52, 52, 52, 52, 52, 1, 1] 52 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003115 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003115/1 /scratch/stefan/7769584/working/building/REAL300000003115 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/129 `/scratch/stefan/7769584/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1) `REAL300000003115.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003115 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 22, 27, 22, 27, 27, 22, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 27, 27, 27, 27, 22, 7, 2, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003115 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 22, 27, 22, 27, 27, 22, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 22, 6, 1, 2, 2, 2, 2, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) 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: REAL300000003115 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 21, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 10, 21, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003115 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003115 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003115/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003115/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003115 Building REAL300000003116 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003116' /scratch/stefan/7769584/working/building/REAL300000003116 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003116 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003116/0 /scratch/stefan/7769584/working/building/REAL300000003116 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/130 `/scratch/stefan/7769584/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2CC(F)(F)F)C=C1) `REAL300000003116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003116 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2CC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [92, 61, 92, 61, 92, 92, 61, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 92, 92, 92, 92, 61, 12, 1, 1, 1, 1, 6, 6, 92, 92] 110 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 383 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: REAL300000003116 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2CC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 43, 43, 96, 96, 69, 96, 96, 96, 110, 110, 110, 110, 1, 1, 1, 1, 11, 43, 96, 96, 70, 96, 110, 110, 1, 1] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 284 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003116 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003116 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003116/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003116 Building REAL300000003117 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003117' /scratch/stefan/7769584/working/building/REAL300000003117 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003117 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003117/0 /scratch/stefan/7769584/working/building/REAL300000003117 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/131 `/scratch/stefan/7769584/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=N1) `REAL300000003117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003117 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 20, 6, 1, 1, 1, 1] 31 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24]) 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: REAL300000003117 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 27, 31, 31, 27, 27, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 1, 7, 27, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003117 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003117 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003117/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003117 Building REAL300000003118 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003118' /scratch/stefan/7769584/working/building/REAL300000003118 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003118 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003118/0 /scratch/stefan/7769584/working/building/REAL300000003118 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/132 `/scratch/stefan/7769584/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1) `REAL300000003118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003118 none O=C([O-])C1=CC=C(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [103, 74, 103, 60, 103, 103, 60, 60, 11, 1, 11, 43, 62, 90, 90, 77, 90, 90, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 11, 45, 45, 62, 61, 90, 90, 90, 90, 90, 1, 1, 1, 1, 103, 103] 186 rigid atoms, others: [38, 39, 40, 9, 41, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 746 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003118 none O=C([O-])C1=CC=C(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [154, 126, 154, 115, 154, 154, 115, 115, 30, 6, 3, 1, 1, 1, 1, 1, 1, 1, 30, 90, 90, 90, 90, 90, 154, 154, 154, 154, 29, 7, 7, 3, 3, 1, 1, 1, 1, 1, 90, 90, 90, 90, 154, 154] 186 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 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: REAL300000003118 none O=C([O-])C1=CC=C(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 35, 79, 112, 140, 140, 120, 140, 140, 35, 91, 91, 91, 91, 91, 1, 1, 1, 1, 35, 85, 85, 108, 112, 140, 140, 140, 140, 140, 91, 91, 91, 91, 1, 1] 159 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003118 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003118/1 /scratch/stefan/7769584/working/building/REAL300000003118 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/133 `/scratch/stefan/7769584/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1) `REAL300000003118.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003118 none O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 87, 41, 87, 87, 41, 9, 9, 1, 9, 68, 89, 108, 108, 89, 108, 108, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 41, 68, 68, 89, 89, 108, 108, 89, 108, 108, 1, 1, 1, 1, 87, 87] 201 rigid atoms, others: [38, 39, 40, 9, 41, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 803 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003118 none O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 142, 170, 123, 170, 170, 123, 34, 34, 7, 3, 1, 1, 1, 1, 1, 1, 1, 34, 108, 108, 108, 108, 108, 170, 170, 170, 170, 123, 7, 7, 3, 3, 1, 1, 1, 1, 1, 108, 108, 108, 108, 170, 170] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39, 40, 41, 42, 43]) total number of confs: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003118 none O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 33, 33, 106, 117, 119, 119, 117, 119, 119, 33, 55, 55, 55, 55, 55, 1, 1, 1, 1, 11, 106, 106, 117, 117, 119, 119, 117, 119, 119, 55, 55, 55, 55, 1, 1] 127 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003118 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003118 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003118/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003118/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003118 Building REAL300000003119 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003119' /scratch/stefan/7769584/working/building/REAL300000003119 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003119 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003119/0 /scratch/stefan/7769584/working/building/REAL300000003119 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/134 `/scratch/stefan/7769584/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CN=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1) `REAL300000003119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003119 none CC(C)(C)OC(=O)NC1=CN=C(C=NNC2=CC=C(C(=O)[O-])C=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', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 34, 39, 33, 33, 33, 33, 26, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 34, 33, 25, 5, 1, 1, 1, 1, 32] 49 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003119 none CC(C)(C)OC(=O)NC1=CN=C(C=NNC2=CC=C(C(=O)[O-])C=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', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 10, 10, 7, 4, 7, 1, 1, 1, 1, 1, 1, 4, 4, 20, 32, 32, 20, 23, 32, 32, 32, 32, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4, 20, 32, 32, 33, 33, 1] 49 rigid atoms, others: [43, 36, 7, 8, 9, 10, 11, 12, 24, 25] 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, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003119 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003119/1 /scratch/stefan/7769584/working/building/REAL300000003119 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/135 `/scratch/stefan/7769584/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CN=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C=N1) `REAL300000003119.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003119 none CC(C)(C)OC(=O)NC1=CN=C(CN=NC2=CC=C(C(=O)[O-])C=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', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 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, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 157, 127, 157, 70, 70, 70, 70, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 70, 18, 18, 1, 1, 1, 1, 70] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003119 none CC(C)(C)OC(=O)NC1=CN=C(CN=NC2=CC=C(C(=O)[O-])C=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', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 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, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 20, 21, 21, 11, 8, 11, 1, 1, 1, 1, 1, 1, 9, 55, 55, 70, 70, 55, 55, 70, 70, 70, 70, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 9, 9, 70, 70, 70, 70, 1] 201 rigid atoms, others: [43, 36, 7, 8, 9, 10, 11, 12, 24, 25] 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, 37, 38, 39, 40, 41, 42]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003119 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003119 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003119/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003119/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003119 Building REAL300000003120 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003120' /scratch/stefan/7769584/working/building/REAL300000003120 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003120 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003120/0 /scratch/stefan/7769584/working/building/REAL300000003120 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/136 `/scratch/stefan/7769584/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1) `REAL300000003120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003120 none O=C([O-])C1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 10, 12, 12, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 12, 10, 1, 1, 1, 1, 1, 1, 1, 12, 12] 12 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003120 none O=C([O-])C1=CC=C(NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 11, 1, 1] 12 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003120 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003120 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003120/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003120 Building REAL300000003121 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003121' /scratch/stefan/7769584/working/building/REAL300000003121 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003121 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003121/0 /scratch/stefan/7769584/working/building/REAL300000003121 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/137 `/scratch/stefan/7769584/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C#N)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003121 none CN(C)C1=CC=C(C#N)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 26, 26, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 26, 7, 1, 1, 1, 1] 32 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 55 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003121 none CN(C)C1=CC=C(C#N)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 32, 32, 30, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 1, 1, 1, 7, 26, 32, 32, 32, 32] 32 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 2, 12, 13, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003121 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003121 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003121/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003121 Building REAL300000003122 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003122' /scratch/stefan/7769584/working/building/REAL300000003122 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003122 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003122/0 /scratch/stefan/7769584/working/building/REAL300000003122 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/138 `/scratch/stefan/7769584/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])C=C1) `REAL300000003122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003122 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 27, 29, 29, 27, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 29, 29, 29, 29, 27, 7, 1, 1, 1, 29, 29] 29 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003122 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 27, 27, 30, 30, 27, 27, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 10, 27, 30, 30, 30, 1, 1] 30 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 33, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003122 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003122 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003122/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003122 Building REAL300000003123 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003123' /scratch/stefan/7769584/working/building/REAL300000003123 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003123 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003123/0 /scratch/stefan/7769584/working/building/REAL300000003123 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/139 `/scratch/stefan/7769584/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC) `REAL300000003123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003123 none COC1=CC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 69, 69, 69, 69, 69, 35, 35, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 69, 69, 81, 81, 81, 81, 69, 35, 7, 1, 1, 1, 1, 69, 81, 81, 81] 81 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) 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: REAL300000003123 none COC1=CC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45, 69, 69, 56, 69, 69, 69, 69, 69, 1, 1, 1, 3, 4, 4, 4, 1, 10, 45, 69, 69, 69, 69, 1, 4, 4, 4] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 33, 19, 20, 21, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003123 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003123 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003123/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003123 Building REAL300000003124 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003124' /scratch/stefan/7769584/working/building/REAL300000003124 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003124 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003124/0 /scratch/stefan/7769584/working/building/REAL300000003124 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/140 `/scratch/stefan/7769584/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2F)C=C1) `REAL300000003124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003124 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 32, 40, 40, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 32, 10, 1, 1, 40, 40] 41 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) 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: REAL300000003124 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 10, 23, 41, 41, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003124 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003124/1 /scratch/stefan/7769584/working/building/REAL300000003124 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/141 `/scratch/stefan/7769584/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NC=C(Br)C=C2F)C=C1) `REAL300000003124.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003124 none O=C([O-])C1=CC=C(N=NCC2=NC=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 8, 8, 1, 1, 47, 47] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003124 none O=C([O-])C1=CC=C(N=NCC2=NC=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 21, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 21, 21, 47, 47, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003124 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003124 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003124/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003124/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003124 Building REAL300000003125 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003125' /scratch/stefan/7769584/working/building/REAL300000003125 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003125 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003125/0 /scratch/stefan/7769584/working/building/REAL300000003125 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/142 `/scratch/stefan/7769584/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCOC3)N=N2)C=C1) `REAL300000003125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003125 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCOC3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 201, 201, 200, 200, 67, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 67, 67, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 408 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003125 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCOC3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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: [56, 46, 56, 44, 56, 56, 44, 44, 8, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 1, 1, 56, 56, 56, 56, 8, 8, 1, 8, 8, 19, 19, 19, 19, 19, 19, 19, 56, 56] 201 rigid atoms, others: [9, 10, 11, 12, 13, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000003125 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCOC3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 22, 57, 57, 57, 140, 201, 201, 201, 201, 57, 57, 1, 1, 1, 1, 22, 22, 57, 140, 140, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003125 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003125 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003125/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003125 Building REAL300000003126 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003126' /scratch/stefan/7769584/working/building/REAL300000003126 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003126 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003126/0 /scratch/stefan/7769584/working/building/REAL300000003126 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/143 `/scratch/stefan/7769584/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(CC(F)(F)F)C=C2)C=C1) `REAL300000003126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003126 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [33, 24, 33, 24, 33, 33, 24, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 33, 33, 33, 33, 24, 7, 1, 1, 4, 4, 1, 1, 33, 33] 44 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) 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: REAL300000003126 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 27, 27, 33, 33, 31, 33, 45, 45, 45, 45, 33, 33, 1, 1, 1, 1, 9, 27, 33, 33, 45, 45, 33, 33, 1, 1] 45 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003126 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003126 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003126/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003126 Building REAL300000003127 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003127' /scratch/stefan/7769584/working/building/REAL300000003127 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003127 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003127/0 /scratch/stefan/7769584/working/building/REAL300000003127 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/144 `/scratch/stefan/7769584/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003127 none CC(C)(C)OC(=O)NCC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 192, 145, 192, 57, 24, 24, 14, 24, 24, 12, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 57, 57, 14, 24, 24, 11, 3, 1, 1, 1, 1, 24] 201 rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003127 none CC(C)(C)OC(=O)NCC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 63, 34, 63, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 24, 24, 16, 16, 24, 24, 24, 24, 1, 74, 74, 74, 73, 73, 73, 74, 74, 74, 34, 6, 6, 1, 1, 1, 7, 16, 24, 24, 24, 24, 1] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 48, 40, 41, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003127 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003127 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003127/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003127 Building REAL300000003128 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003128' /scratch/stefan/7769584/working/building/REAL300000003128 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003128 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003128/0 /scratch/stefan/7769584/working/building/REAL300000003128 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/145 `/scratch/stefan/7769584/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)N1) `REAL300000003128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003128 none CCOC(=O)C1=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 185, 96, 185, 96, 96, 96, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 201, 201, 201, 201, 201, 96, 96, 96, 33, 6, 1, 1, 1, 1, 96, 96, 96, 96] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 489 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003128 none CCOC(=O)C1=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 14, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 62, 96, 96, 62, 67, 96, 96, 96, 96, 1, 1, 1, 31, 31, 31, 30, 30, 2, 2, 2, 13, 62, 96, 96, 96, 96, 2, 2, 2, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 41, 21, 22, 23] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003128 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003128 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003128/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003128 Building REAL300000003129 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003129' /scratch/stefan/7769584/working/building/REAL300000003129 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003129 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003129/0 /scratch/stefan/7769584/working/building/REAL300000003129 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/146 `/scratch/stefan/7769584/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=C21) `REAL300000003129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003129 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 48, 34, 6, 1, 1, 1, 1, 49, 49, 49] 49 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) 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: REAL300000003129 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 40, 48, 49, 42, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 39, 48, 48, 49, 49, 1, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 26] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003129 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003129/1 /scratch/stefan/7769584/working/building/REAL300000003129 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/147 `/scratch/stefan/7769584/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=C21) `REAL300000003129.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003129 none CN1C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 7, 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 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, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 12, 1, 1, 1, 1, 44, 44, 44] 44 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003129 none CN1C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 7, 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 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, 9, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 9, 44, 44, 44, 44, 1, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 26] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003129 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003129 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003129/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003129/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003129 Building REAL300000003130 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003130' /scratch/stefan/7769584/working/building/REAL300000003130 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003130 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003130/0 /scratch/stefan/7769584/working/building/REAL300000003130 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/148 `/scratch/stefan/7769584/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1) `REAL300000003130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003130 none CCOC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 141, 135, 70, 135, 70, 70, 69, 39, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 153, 153, 153, 153, 153, 70, 70, 38, 6, 1, 1, 1, 1, 69] 153 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003130 none CCOC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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: [34, 20, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 39, 69, 69, 41, 41, 70, 70, 70, 70, 1, 34, 34, 34, 34, 34, 1, 1, 6, 39, 69, 69, 70, 70, 1] 153 rigid atoms, others: [3, 5, 6, 7, 8, 9, 35, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003130 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003130 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003130/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003130 Building REAL300000003131 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003131' /scratch/stefan/7769584/working/building/REAL300000003131 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003131 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003131/0 /scratch/stefan/7769584/working/building/REAL300000003131 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/149 `/scratch/stefan/7769584/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CNC2=CC=CC=C12)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003131 none CC(CCC1=CNC2=CC=CC=C12)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', '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, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [30, 4, 30, 75, 91, 186, 186, 186, 186, 186, 186, 186, 186, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 78, 78, 91, 88, 186, 186, 186, 186, 186, 186, 1, 1, 1, 1] 186 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 510 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: REAL300000003131 none CC(CCC1=CNC2=CC=CC=C12)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', '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, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 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: [60, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 181, 181, 186, 186, 181, 186, 186, 186, 186, 186, 60, 60, 60, 60, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186] 186 rigid atoms, others: [32, 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, 38, 39, 40, 41]) total number of confs: 442 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003131 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003131 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003131/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003131 Building REAL300000003132 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003132' /scratch/stefan/7769584/working/building/REAL300000003132 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003132 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003132/0 /scratch/stefan/7769584/working/building/REAL300000003132 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/150 `/scratch/stefan/7769584/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1) `REAL300000003132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003132 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=CC=C(Cl)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 19, 67, 67, 173, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 67, 67, 67, 173, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 503 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003132 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=CC=C(Cl)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 36, 79, 79, 45, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 7, 7, 7, 35, 79, 79, 79, 79, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 35, 36, 41, 42, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 313 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: REAL300000003132 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=CC=C(Cl)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 79, 79, 45, 79, 196, 201, 201, 201, 201, 201, 201, 79, 79, 25, 25, 25, 6, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 79, 79] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 11, 12, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 448 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003132 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003132 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003132/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003132 Building REAL300000003133 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003133' /scratch/stefan/7769584/working/building/REAL300000003133 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003133 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003133/0 /scratch/stefan/7769584/working/building/REAL300000003133 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/151 `/scratch/stefan/7769584/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CS1) `REAL300000003133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003133 none CC(C)(C)OC(=O)NC1=NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CS1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 64, 50, 64, 45, 45, 45, 28, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 45, 92, 92, 92, 92, 92, 92, 92, 92, 92, 50, 27, 5, 1, 1, 1, 1, 44] 92 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) 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: REAL300000003133 none CC(C)(C)OC(=O)NC1=NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CS1 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 13, 13, 4, 2, 5, 1, 1, 1, 1, 1, 6, 6, 33, 44, 45, 33, 33, 45, 45, 45, 45, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 6, 32, 44, 44, 45, 45, 1] 92 rigid atoms, others: [7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003133 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003133 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003133/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003133 Building REAL300000003134 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003134' /scratch/stefan/7769584/working/building/REAL300000003134 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003134 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003134/0 /scratch/stefan/7769584/working/building/REAL300000003134 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/152 `/scratch/stefan/7769584/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C2CCC1CC(CN=NC1=CC=C(C(=O)[O-])C=C1)C2) `REAL300000003134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003134 none CC(C)(C)OC(=O)N1C2CCC1CC(CN=NC1=CC=C(C(=O)[O-])C=C1)C2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 30, 21, 30, 21, 21, 21, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 21, 21] 47 rigid atoms, others: [48, 49, 50, 47, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52]) total number of confs: 133 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: REAL300000003134 none CC(C)(C)OC(=O)N1C2CCC1CC(CN=NC1=CC=C(C(=O)[O-])C=C1)C2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [15, 13, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 21, 21, 15, 15, 21, 21, 21, 21, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 1, 1] 47 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 40, 51, 52, 41, 39, 26, 42, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 109 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003134 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003134 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003134/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003134 Building REAL300000003135 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003135' /scratch/stefan/7769584/working/building/REAL300000003135 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003135 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003135/0 /scratch/stefan/7769584/working/building/REAL300000003135 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/153 `/scratch/stefan/7769584/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC(CN=NC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000003135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003135 none CC(C)(C)OC(=O)NC1CC(CN=NC2=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 193, 159, 193, 73, 73, 73, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 73, 73, 73, 73, 21, 21, 1, 1, 1, 1, 73, 73] 201 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) 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: REAL300000003135 none CC(C)(C)OC(=O)NC1CC(CN=NC2=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 25, 25, 15, 8, 15, 1, 1, 1, 1, 1, 9, 56, 56, 73, 73, 56, 56, 73, 73, 73, 73, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 1, 1, 1, 9, 9, 73, 73, 73, 73, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003135 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003135 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003135/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003135 Building REAL300000003136 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003136' /scratch/stefan/7769584/working/building/REAL300000003136 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003136 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003136/0 /scratch/stefan/7769584/working/building/REAL300000003136 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/154 `/scratch/stefan/7769584/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(N2CCC(CN=NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1) `REAL300000003136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003136 none CN1C=C(N2CCC(CN=NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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, 8, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 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, 63, 63, 63, 63, 31, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 63, 124, 124, 124, 124, 124, 124, 63, 63, 63, 63, 63, 31, 31, 1, 1, 1, 1, 63, 63, 124] 124 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 295 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003136 none CN1C=C(N2CCC(CN=NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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, 8, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 1, 1, 10, 49, 49, 63, 63, 49, 52, 63, 63, 63, 63, 1, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 10, 10, 63, 63, 63, 63, 1, 1, 12] 124 rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 39, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 206 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: REAL300000003136 none CN1C=C(N2CCC(CN=NC3=CC=C(C(=O)[O-])C=C3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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, 8, 1, 1, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 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, 12, 12, 12, 12, 53, 122, 122, 124, 124, 122, 124, 124, 124, 124, 124, 12, 1, 1, 2, 2, 2, 1, 12, 12, 12, 12, 12, 53, 53, 124, 124, 124, 124, 12, 12, 1] 124 rigid atoms, others: [0, 1, 2, 3, 4, 40, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 288 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003136 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003136 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003136/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003136 Building REAL300000003137 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003137' /scratch/stefan/7769584/working/building/REAL300000003137 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003137 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003137/0 /scratch/stefan/7769584/working/building/REAL300000003137 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/155 `/scratch/stefan/7769584/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=C(Cl)N=CC=C2O1) `REAL300000003137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003137 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 50, 50, 51, 51, 50, 50, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 51, 51, 51, 51, 1, 1, 1] 51 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003137 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [27, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 51, 51, 51, 51, 51, 51, 51, 51, 51, 27, 27, 27, 27, 1, 1, 1, 1, 51, 51, 51] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003137 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003137 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003137/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003137 Building REAL300000003138 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003138' /scratch/stefan/7769584/working/building/REAL300000003138 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003138 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003138/0 /scratch/stefan/7769584/working/building/REAL300000003138 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/156 `/scratch/stefan/7769584/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=C1OC) `REAL300000003138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003138 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 9, 1, 9, 9, 45, 101, 101, 45, 45, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 3, 1, 1, 6, 23, 23, 23, 23, 23, 45, 101, 101, 101, 101, 1, 1, 1, 4, 4, 4, 6, 6, 6] 130 rigid atoms, others: [2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 552 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: REAL300000003138 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 101, 101, 101, 101, 101, 120, 101, 101, 126, 75, 75, 75, 74, 74, 5, 1, 1, 1, 1, 101, 101, 101, 120, 120, 120, 126, 126, 126] 130 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 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: 441 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003138 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003138/1 /scratch/stefan/7769584/working/building/REAL300000003138 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/157 `/scratch/stefan/7769584/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=C1OC) `REAL300000003138.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003138 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 6, 1, 6, 29, 29, 46, 46, 29, 29, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 4, 1, 1, 4, 11, 11, 11, 11, 11, 6, 46, 46, 46, 46, 1, 1, 1, 4, 4, 4, 5, 5, 5] 75 rigid atoms, others: [2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) 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: REAL300000003138 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 26, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 46, 46, 46, 46, 46, 74, 46, 46, 74, 37, 37, 37, 37, 37, 26, 1, 1, 1, 1, 46, 46, 46, 74, 74, 74, 74, 74, 74] 75 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 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: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003138 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003138 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003138/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003138/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003138 Building REAL300000003139 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003139' /scratch/stefan/7769584/working/building/REAL300000003139 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003139 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003139/0 /scratch/stefan/7769584/working/building/REAL300000003139 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/158 `/scratch/stefan/7769584/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1C[C@@H](CN=NC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000003139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003139 none CC(C)(C)OC(=O)N[C@H]1C[C@@H](CN=NC2=CC=C(C(=O)[O-])C=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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 192, 166, 192, 73, 73, 73, 73, 22, 73, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 73, 73, 22, 22, 1, 1, 1, 1, 73, 73] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003139 none CC(C)(C)OC(=O)N[C@H]1C[C@@H](CN=NC2=CC=C(C(=O)[O-])C=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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 9, 56, 56, 73, 73, 56, 56, 73, 73, 73, 73, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 1, 1, 9, 9, 73, 73, 73, 73, 1, 1] 201 rigid atoms, others: [45, 36, 37, 7, 8, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003139 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003139 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003139/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003139 Building REAL300000003140 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003140' /scratch/stefan/7769584/working/building/REAL300000003140 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003140 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003140/0 /scratch/stefan/7769584/working/building/REAL300000003140 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/159 `/scratch/stefan/7769584/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1) `REAL300000003140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003140 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 49, 39, 49, 49, 39, 21, 21, 3, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 49, 49, 49, 49, 39, 21, 4, 4, 1, 1, 1, 1, 1, 4, 49, 49] 49 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003140 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 38, 48, 38, 48, 48, 38, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 48, 48, 48, 48, 38, 8, 1, 1, 4, 4, 1, 4, 4, 1, 48, 48] 49 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003140 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 51, 51, 45, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 9, 31, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003140 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003140 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003140/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003140 Building REAL300000003141 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003141' /scratch/stefan/7769584/working/building/REAL300000003141 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003141 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003141/0 /scratch/stefan/7769584/working/building/REAL300000003141 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/160 `/scratch/stefan/7769584/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C(F)=C2F)C=C1) `REAL300000003141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003141 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 17, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 25, 25, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 22, 7, 1, 1, 25, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003141 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 17, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 24, 25, 25, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003141 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003141 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003141/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003141 Building REAL300000003142 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003142' /scratch/stefan/7769584/working/building/REAL300000003142 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003142 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003142/0 /scratch/stefan/7769584/working/building/REAL300000003142 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/161 `/scratch/stefan/7769584/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003142 none COC1=NC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 21, 21, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 21, 7, 1, 1, 1, 1] 27 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003142 none COC1=NC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 27, 27, 22, 27, 27, 27, 27, 27, 3, 3, 3, 1, 1, 8, 22, 27, 27, 27, 27] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/7769584/working/building/REAL300000003142 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003142 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003142/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003142 Building REAL300000003143 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003143' /scratch/stefan/7769584/working/building/REAL300000003143 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003143 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003143/0 /scratch/stefan/7769584/working/building/REAL300000003143 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/162 `/scratch/stefan/7769584/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)OC(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003143 none CN1N=C(C(=O)OC(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 122, 122, 163, 163, 163, 163, 74, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 74, 74, 74, 163, 163, 163, 163, 163, 163, 163, 163, 163, 74, 33, 7, 1, 1, 1, 1] 163 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 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: REAL300000003143 none CN1N=C(C(=O)OC(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 24, 28, 29, 28, 1, 1, 1, 8, 8, 44, 74, 74, 50, 74, 74, 74, 74, 74, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 8, 44, 74, 74, 74, 74] 163 rigid atoms, others: [0, 1, 2, 3, 4, 37, 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, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003143 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003143 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003143/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003143 Building REAL300000003144 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003144' /scratch/stefan/7769584/working/building/REAL300000003144 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003144 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003144/0 /scratch/stefan/7769584/working/building/REAL300000003144 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/163 `/scratch/stefan/7769584/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Br)SC=C2)C=C1) `REAL300000003144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003144 none O=C([O-])C1=CC=C(NN=CC2=C(Br)SC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 28, 28, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 26, 10, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 24, 25]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003144 none O=C([O-])C1=CC=C(NN=CC2=C(Br)SC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 20, 20, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 20, 28, 28, 1, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003144 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003144 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003144/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003144 Building REAL300000003145 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003145' /scratch/stefan/7769584/working/building/REAL300000003145 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003145 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003145/0 /scratch/stefan/7769584/working/building/REAL300000003145 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/164 `/scratch/stefan/7769584/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1OC) `REAL300000003145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003145 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1OC NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 162, 78, 78, 78, 36, 35, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 77, 78, 133, 187, 187, 187, 187, 187, 77, 35, 5, 1, 1, 1, 1, 78, 133, 133, 133] 187 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 483 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: REAL300000003145 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1OC NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [42, 9, 1, 1, 1, 1, 1, 7, 7, 39, 77, 77, 39, 39, 77, 77, 77, 77, 1, 1, 1, 1, 1, 3, 43, 43, 43, 42, 42, 1, 7, 39, 78, 78, 77, 77, 1, 4, 4, 4] 187 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 36, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 507 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003145 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003145 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003145/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003145 Building REAL300000003146 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003146' /scratch/stefan/7769584/working/building/REAL300000003146 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003146 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003146/0 /scratch/stefan/7769584/working/building/REAL300000003146 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/165 `/scratch/stefan/7769584/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C3=CC=CC=C23)C=C1) `REAL300000003146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003146 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 33, 37, 37, 32, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 32, 12, 1, 1, 1, 1, 1, 1, 37, 37] 37 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 21, 22, 23, 24, 25, 26]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003146 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 11, 21, 37, 37, 37, 37, 37, 37, 1, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003146 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003146 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003146/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003146 Building REAL300000003147 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003147' /scratch/stefan/7769584/working/building/REAL300000003147 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003147 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003147/0 /scratch/stefan/7769584/working/building/REAL300000003147 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/166 `/scratch/stefan/7769584/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CN=C2Br)C=C1) `REAL300000003147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003147 none O=C([O-])C1=CC=C(NN=CC2=CC=CN=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 23, 27, 27, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 23, 8, 1, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003147 none O=C([O-])C1=CC=C(NN=CC2=CC=CN=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 19, 19, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 19, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003147 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003147 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003147/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003147 Building REAL300000003148 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003148' /scratch/stefan/7769584/working/building/REAL300000003148 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003148 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003148/0 /scratch/stefan/7769584/working/building/REAL300000003148 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/167 `/scratch/stefan/7769584/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)C=C1) `REAL300000003148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003148 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations 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, 173, 61, 61, 23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 173, 61, 23, 23, 7, 7, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 490 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003148 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 92, 104, 75, 104, 104, 67, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 104, 104, 105, 105, 67, 8, 1, 1, 7, 7, 16, 16, 16, 16, 104, 104] 201 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 15] 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, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003148 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 42, 43, 115, 115, 115, 115, 115, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 42, 115, 115, 197, 197, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003148 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003148 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003148/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003148 Building REAL300000003149 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003149' /scratch/stefan/7769584/working/building/REAL300000003149 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003149 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003149/0 /scratch/stefan/7769584/working/building/REAL300000003149 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/168 `/scratch/stefan/7769584/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2OC(F)(F)F)C=C1) `REAL300000003149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003149 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 25, 11, 25, 25, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 25, 25, 25, 25, 11, 5, 1, 1, 1, 25, 25] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) 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: REAL300000003149 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 53, 53, 53, 53, 53, 53, 53, 78, 78, 78, 78, 1, 1, 1, 1, 6, 27, 53, 53, 53, 1, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003149 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003149 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003149/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003149 Building REAL300000003150 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003150' /scratch/stefan/7769584/working/building/REAL300000003150 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003150 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003150/0 /scratch/stefan/7769584/working/building/REAL300000003150 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/169 `/scratch/stefan/7769584/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003150 none CC(C)OC1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 54, 80, 80, 80, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 80, 54, 80, 37, 6, 1, 1, 1, 1] 111 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 236 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: REAL300000003150 none CC(C)OC1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 48, 80, 80, 48, 49, 80, 80, 80, 80, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 12, 48, 80, 80, 80, 80] 111 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 12, 13, 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: 401 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003150 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003150 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003150/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003150 Building REAL300000003151 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003151' /scratch/stefan/7769584/working/building/REAL300000003151 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003151 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003151/0 /scratch/stefan/7769584/working/building/REAL300000003151 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/170 `/scratch/stefan/7769584/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(F)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003151 none CCOC1=CC(F)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 143, 109, 109, 108, 109, 109, 109, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 144, 144, 144, 144, 144, 109, 109, 37, 6, 1, 1, 1, 1, 108] 144 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 224 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: REAL300000003151 none CCOC1=CC(F)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 60, 108, 108, 60, 68, 108, 108, 108, 108, 1, 18, 18, 18, 18, 18, 1, 1, 11, 60, 109, 109, 108, 108, 1] 144 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 27, 28] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 516 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003151 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003151 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003151/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003151 Building REAL300000003152 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003152' /scratch/stefan/7769584/working/building/REAL300000003152 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003152 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003152/0 /scratch/stefan/7769584/working/building/REAL300000003152 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/171 `/scratch/stefan/7769584/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1) `REAL300000003152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003152 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 19, 19, 6, 6, 14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 14, 14, 36, 36, 36, 36, 36, 19, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 36, 36] 36 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 114 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003152 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 15, 22, 15, 22, 22, 15, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 1, 1, 22, 22, 22, 22, 15, 4, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 22, 22] 36 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 118 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003152 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 19, 19, 26, 26, 20, 20, 36, 36, 36, 36, 36, 36, 26, 26, 1, 1, 1, 1, 6, 19, 26, 26, 36, 36, 36, 36, 36, 36, 36, 36, 26, 26, 1, 1] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003152 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003152 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003152/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003152 Building REAL300000003153 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003153' /scratch/stefan/7769584/working/building/REAL300000003153 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003153 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003153/0 /scratch/stefan/7769584/working/building/REAL300000003153 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/172 `/scratch/stefan/7769584/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2F)C=C1) `REAL300000003153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003153 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [83, 49, 84, 47, 84, 84, 44, 8, 8, 1, 1, 1, 1, 1, 1, 12, 52, 52, 1, 1, 1, 83, 83, 84, 84, 44, 8, 1, 1, 52, 1, 83, 83] 197 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 20, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 31]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003153 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 41, 42, 80, 80, 47, 80, 188, 199, 199, 80, 80, 80, 1, 1, 1, 1, 10, 41, 79, 80, 199, 80, 1, 1] 199 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003153 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003153 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003153/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003153 Building REAL300000003154 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003154' /scratch/stefan/7769584/working/building/REAL300000003154 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003154 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003154/0 /scratch/stefan/7769584/working/building/REAL300000003154 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/173 `/scratch/stefan/7769584/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003154 none CC(C)(C)OC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 54, 62, 62, 32, 32, 32, 32, 32, 17, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 62, 62, 62, 62, 62, 62, 62, 62, 62, 32, 32, 32, 16, 5, 1, 1, 1, 1, 32] 62 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 146 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: REAL300000003154 none CC(C)(C)OC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 32, 32, 27, 28, 32, 32, 32, 32, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 7, 25, 32, 32, 32, 32, 1] 62 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 22, 41] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003154 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003154 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003154/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003154 Building REAL300000003155 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003155' /scratch/stefan/7769584/working/building/REAL300000003155 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003155 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003155/0 /scratch/stefan/7769584/working/building/REAL300000003155 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/174 `/scratch/stefan/7769584/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=C1C) `REAL300000003155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003155 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=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', 'C.2', 'O.co2', 'O.co2', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 7, 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, 22, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 30, 31, 31, 31, 31, 31, 21, 6, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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: REAL300000003155 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(F)C=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', 'C.2', 'O.co2', 'O.co2', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 7, 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, 1, 1, 1, 1, 6, 6, 25, 30, 30, 25, 26, 30, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 3, 1, 6, 25, 31, 31, 30, 30, 1, 2, 2, 2] 31 rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003155 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003155 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003155/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003155 Building REAL300000003156 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003156' /scratch/stefan/7769584/working/building/REAL300000003156 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003156 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003156/0 /scratch/stefan/7769584/working/building/REAL300000003156 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/175 `/scratch/stefan/7769584/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Br) `REAL300000003156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003156 none CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 36, 36, 24, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 6, 1, 1, 1, 1, 36, 36, 36] 36 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 17, 18, 19, 20, 21, 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: REAL300000003156 none CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 17, 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, 2, 2, 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, 10, 10, 32, 36, 36, 32, 32, 36, 36, 36, 36, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 32, 36, 36, 36, 36, 2, 2, 2] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003156 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003156 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003156/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003156 Building REAL300000003157 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003157' /scratch/stefan/7769584/working/building/REAL300000003157 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003157 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003157/0 /scratch/stefan/7769584/working/building/REAL300000003157 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/176 `/scratch/stefan/7769584/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003157 none CC1=CC=NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 29, 6, 1, 1, 1, 1] 42 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003157 none CC1=CC=NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 42, 42, 37, 37, 42, 42, 42, 42, 1, 1, 2, 2, 2, 1, 1, 10, 37, 42, 42, 42, 42] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003157 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003157/1 /scratch/stefan/7769584/working/building/REAL300000003157 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/177 `/scratch/stefan/7769584/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003157.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003157 none CC1=CC=NC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 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, 20, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 38, 20, 20, 1, 1, 1, 1] 38 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003157 none CC1=CC=NC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 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, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 2, 2, 2, 1, 1, 8, 8, 38, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003157 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003157 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003157/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003157/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003157 Building REAL300000003158 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003158' /scratch/stefan/7769584/working/building/REAL300000003158 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003158 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003158/0 /scratch/stefan/7769584/working/building/REAL300000003158 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/178 `/scratch/stefan/7769584/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(F)C=C1[N+](=O)[O-])N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003158 none CC(CC1=CC=C(F)C=C1[N+](=O)[O-])N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [20, 4, 20, 36, 43, 43, 36, 43, 43, 43, 43, 43, 43, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 36, 36, 43, 43, 43, 1, 1, 1, 1] 43 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 199 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: REAL300000003158 none CC(CC1=CC=C(F)C=C1[N+](=O)[O-])N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 11, 11, 6, 6, 1, 1, 1, 43, 43, 43, 43] 43 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003158 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003158 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003158/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003158 Building REAL300000003159 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003159' /scratch/stefan/7769584/working/building/REAL300000003159 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003159 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003159/0 /scratch/stefan/7769584/working/building/REAL300000003159 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/179 `/scratch/stefan/7769584/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(CCN=NC1=CC=C(C(=O)[O-])C=C1)CC1=CC=CC=C1) `REAL300000003159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003159 none CC(C)(C)OC(=O)NC(CCN=NC1=CC=C(C(=O)[O-])C=C1)CC1=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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 34, 29, 17, 29, 6, 1, 6, 20, 26, 100, 100, 126, 126, 100, 100, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 6, 20, 20, 26, 26, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [54, 8, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003159 none CC(C)(C)OC(=O)NC(CCN=NC1=CC=C(C(=O)[O-])C=C1)CC1=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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [136, 136, 136, 136, 131, 105, 131, 79, 19, 24, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 82, 126, 126, 126, 126, 126, 126, 136, 136, 136, 136, 136, 136, 136, 136, 136, 105, 78, 33, 33, 24, 24, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126] 166 rigid atoms, others: [45, 12, 46, 44, 13, 14, 15, 16, 17, 20, 21, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003159 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003159 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003159/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003159 Building REAL300000003160 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003160' /scratch/stefan/7769584/working/building/REAL300000003160 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003160 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003160/0 /scratch/stefan/7769584/working/building/REAL300000003160 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/180 `/scratch/stefan/7769584/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NN=CN2CC2=CC=CC=C2)C=C1) `REAL300000003160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003160 none O=C([O-])C1=CC=C(N=NCC2=NN=CN2CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 199, 201, 201, 199, 199, 64, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 64, 64, 16, 5, 5, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 420 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003160 none O=C([O-])C1=CC=C(N=NCC2=NN=CN2CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 68, 82, 55, 82, 82, 55, 55, 8, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 8, 16, 16, 82, 82, 82, 82, 8, 8, 1, 8, 8, 16, 16, 8, 16, 16, 82, 82] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 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, 35, 36, 37]) total number of confs: 327 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003160 none O=C([O-])C1=CC=C(N=NCC2=NN=CN2CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 35, 89, 89, 89, 89, 89, 194, 196, 196, 194, 196, 196, 1, 1, 1, 1, 35, 35, 89, 194, 194, 196, 196, 194, 196, 196, 1, 1] 196 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 637 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003160 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003160 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003160/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003160 Building REAL300000003161 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003161' /scratch/stefan/7769584/working/building/REAL300000003161 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003161 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003161/0 /scratch/stefan/7769584/working/building/REAL300000003161 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/181 `/scratch/stefan/7769584/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=CN=C12) `REAL300000003161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003161 none COC(=O)C1=CC=CC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 100, 159, 100, 100, 100, 100, 100, 38, 38, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 100, 100, 100, 100, 159, 159, 159, 100, 100, 100, 38, 7, 1, 1, 1, 1, 100, 100] 159 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003161 none COC(=O)C1=CC=CC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 67, 100, 100, 67, 85, 100, 100, 100, 100, 1, 1, 1, 1, 13, 13, 13, 1, 1, 1, 12, 67, 100, 100, 100, 100, 1, 1] 159 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 39, 22, 23, 24, 25, 38, 29, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003161 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003161 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003161/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003161 Building REAL300000003162 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003162' /scratch/stefan/7769584/working/building/REAL300000003162 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003162 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003162/0 /scratch/stefan/7769584/working/building/REAL300000003162 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/182 `/scratch/stefan/7769584/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)C=C1) `REAL300000003162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003162 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 119, 119, 52, 52, 64, 64, 29, 9, 6, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 119, 64, 64, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 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, 45, 46, 47, 48]) total number of confs: 574 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003162 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 17, 27, 27, 17, 4, 4, 1, 1, 1, 1, 1, 1, 6, 20, 39, 64, 64, 64, 64, 64, 1, 1, 27, 27, 27, 27, 17, 4, 1, 1, 20, 20, 39, 39, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 27, 27] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 45, 46, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 284 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: REAL300000003162 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 14, 14, 22, 22, 14, 19, 64, 113, 152, 201, 201, 201, 201, 201, 22, 22, 1, 1, 1, 1, 4, 14, 22, 22, 113, 113, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 48, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 636 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003162 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003162 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003162/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003162 Building REAL300000003163 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003163' /scratch/stefan/7769584/working/building/REAL300000003163 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003163 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003163/0 /scratch/stefan/7769584/working/building/REAL300000003163 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/183 `/scratch/stefan/7769584/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)OC(C)(C)C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003163 none CN1N=CC(C(=O)OC(C)(C)C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 123, 123, 144, 144, 144, 144, 32, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 144, 144, 144, 144, 144, 144, 144, 144, 144, 31, 5, 1, 1, 1, 1] 144 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003163 none CN1N=CC(C(=O)OC(C)(C)C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 22, 28, 28, 28, 1, 1, 8, 8, 34, 70, 70, 37, 41, 70, 70, 70, 70, 2, 2, 2, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 34, 70, 70, 70, 70] 144 rigid atoms, others: [0, 1, 2, 3, 4, 5, 12, 13, 28] set([6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003163 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003163 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003163/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003163 Building REAL300000003164 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003164' /scratch/stefan/7769584/working/building/REAL300000003164 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003164 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003164/0 /scratch/stefan/7769584/working/building/REAL300000003164 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/184 `/scratch/stefan/7769584/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1) `REAL300000003164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003164 none N#CC1=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 16, 16, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 21, 16, 6, 1, 1, 1, 1, 21, 21, 21, 21, 21] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003164 none N#CC1=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 16, 21, 21, 16, 16, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 9, 16, 21, 21, 21, 21, 1, 1, 1, 1, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 20, 21, 22, 33, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003164 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003164 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003164/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003164 Building REAL300000003165 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003165' /scratch/stefan/7769584/working/building/REAL300000003165 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003165 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003165/0 /scratch/stefan/7769584/working/building/REAL300000003165 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/185 `/scratch/stefan/7769584/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=C(F)C=C(Cl)C=C23)C=C1) `REAL300000003165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003165 none O=C([O-])C1=CC=C(NN=CC2=CNC3=C(F)C=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 43, 46, 46, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 40, 8, 1, 1, 1, 1, 46, 46] 46 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003165 none O=C([O-])C1=CC=C(NN=CC2=CNC3=C(F)C=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 35, 35, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 9, 35, 46, 46, 46, 46, 1, 1] 46 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003165 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003165/1 /scratch/stefan/7769584/working/building/REAL300000003165 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/186 `/scratch/stefan/7769584/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CNC3=C(F)C=C(Cl)C=C23)C=C1) `REAL300000003165.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003165 none O=C([O-])C1=CC=C(N=NCC2=CNC3=C(F)C=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 9, 9, 1, 1, 1, 1, 44, 44] 44 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003165 none O=C([O-])C1=CC=C(N=NCC2=CNC3=C(F)C=C(Cl)C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 14, 14, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003165 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003165 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003165/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003165/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003165 Building REAL300000003166 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003166' /scratch/stefan/7769584/working/building/REAL300000003166 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003166 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003166/0 /scratch/stefan/7769584/working/building/REAL300000003166 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/187 `/scratch/stefan/7769584/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1) `REAL300000003166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003166 none CC(C)(C)OC(=O)NC1=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CNC2=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.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 15, 10, 15, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7] 20 rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003166 none CC(C)(C)OC(=O)NC1=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CNC2=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.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 5, 3, 5, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 20 rigid atoms, others: [7, 8, 9, 10, 11, 45, 46, 47, 48, 49, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003166 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003166/1 /scratch/stefan/7769584/working/building/REAL300000003166 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/188 `/scratch/stefan/7769584/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=C2C(CN=NC3=CC=C(C(=O)[O-])C=C3)=CNC2=CC=C1) `REAL300000003166.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003166 none CC(C)(C)OC(=O)NC1=C2C(CN=NC3=CC=C(C(=O)[O-])C=C3)=CNC2=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.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.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, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 118, 156, 61, 61, 61, 21, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 61, 61, 61, 61, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 21, 21, 1, 1, 1, 1, 61, 61, 61, 61, 61] 201 rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 544 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: REAL300000003166 none CC(C)(C)OC(=O)NC1=C2C(CN=NC3=CC=C(C(=O)[O-])C=C3)=CNC2=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.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.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, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 20, 20, 10, 6, 10, 1, 1, 1, 1, 1, 8, 49, 49, 61, 61, 49, 49, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 8, 8, 61, 61, 61, 61, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 8, 9, 10, 11, 45, 46, 47, 48, 49, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 231 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003166 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003166 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003166/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003166/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003166 Building REAL300000003167 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003167' /scratch/stefan/7769584/working/building/REAL300000003167 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003167 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003167/0 /scratch/stefan/7769584/working/building/REAL300000003167 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/189 `/scratch/stefan/7769584/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CN=CC2=CC=CC=C21)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003167 none CC(CCC1=CN=CC2=CC=CC=C21)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 5, 27, 64, 74, 114, 114, 114, 114, 114, 114, 114, 114, 113, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 67, 67, 71, 74, 114, 114, 114, 114, 114, 114, 1, 1, 1, 1] 114 rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 361 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: REAL300000003167 none CC(CCC1=CN=CC2=CC=CC=C21)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 112, 112, 114, 114, 112, 112, 114, 114, 114, 114, 37, 37, 37, 37, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114] 114 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 38, 37] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42]) total number of confs: 264 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003167 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003167 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003167/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003167 Building REAL300000003168 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003168' /scratch/stefan/7769584/working/building/REAL300000003168 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003168 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003168/0 /scratch/stefan/7769584/working/building/REAL300000003168 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/190 `/scratch/stefan/7769584/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(CC(C)CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003168 none CCCC1=CC=C(CC(C)CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 122, 122, 196, 196, 122, 71, 23, 68, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 196, 196, 201, 201, 201, 201, 201, 201, 201, 196, 196, 121, 120, 78, 78, 78, 78, 23, 23, 1, 1, 1, 1, 196, 196] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 1410 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003168 none CCCC1=CC=C(CC(C)CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 3, 11, 11, 46, 170, 170, 196, 196, 170, 170, 196, 196, 196, 196, 1, 1, 6, 6, 6, 5, 5, 3, 3, 1, 1, 3, 3, 11, 11, 11, 11, 46, 46, 196, 196, 196, 196, 1, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 45, 46, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003168 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003168 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003168/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003168 Building REAL300000003169 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003169' /scratch/stefan/7769584/working/building/REAL300000003169 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003169 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003169/0 /scratch/stefan/7769584/working/building/REAL300000003169 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/191 `/scratch/stefan/7769584/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C=CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1C) `REAL300000003169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003169 none CCOC(=O)C=CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1C 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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 196, 107, 196, 107, 30, 30, 30, 30, 16, 16, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 201, 201, 201, 201, 201, 107, 107, 30, 30, 16, 6, 1, 1, 1, 1, 30, 30, 30] 201 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003169 none CCOC(=O)C=CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1C 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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 69, 52, 10, 52, 10, 1, 1, 1, 1, 1, 1, 7, 7, 22, 30, 30, 22, 30, 30, 30, 30, 30, 1, 1, 110, 110, 110, 110, 110, 10, 10, 1, 1, 7, 21, 30, 30, 30, 30, 2, 2, 2] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003169 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003169 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003169/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003169 Building REAL300000003170 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003170' /scratch/stefan/7769584/working/building/REAL300000003170 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003170 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003170/0 /scratch/stefan/7769584/working/building/REAL300000003170 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/192 `/scratch/stefan/7769584/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1) `REAL300000003170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003170 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 98, 97, 17, 97, 5, 5, 5, 5, 5, 7, 7, 18, 24, 24, 18, 18, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 5, 160, 160, 160, 160, 160, 17, 17, 5, 7, 18, 24, 24, 24, 24, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 664 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003170 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 147, 39, 147, 18, 18, 18, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 24, 24, 21, 24, 24, 18, 201, 201, 201, 201, 201, 39, 39, 18, 15, 4, 1, 1, 1, 1, 24, 24, 23, 24, 24] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) 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: REAL300000003170 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 52, 8, 52, 1, 1, 1, 1, 1, 4, 4, 13, 18, 18, 13, 13, 18, 18, 18, 18, 1, 1, 5, 5, 2, 5, 5, 1, 106, 106, 106, 106, 106, 8, 8, 1, 4, 13, 18, 18, 18, 18, 5, 5, 2, 5, 5] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 21, 22, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003170 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003170 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003170/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003170 Building REAL300000003171 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003171' /scratch/stefan/7769584/working/building/REAL300000003171 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003171 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003171/0 /scratch/stefan/7769584/working/building/REAL300000003171 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/193 `/scratch/stefan/7769584/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCC3=CC=CC4=CC=CC2=C43)C=C1) `REAL300000003171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003171 none O=C([O-])C1=CC=C(NN=C2CCC3=CC=CC4=CC=CC2=C43)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 9, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 38, 37]) total number of confs: 72 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: REAL300000003171 none O=C([O-])C1=CC=C(NN=C2CCC3=CC=CC4=CC=CC2=C43)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 31 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003171 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003171 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003171/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003171 Building REAL300000003172 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003172' /scratch/stefan/7769584/working/building/REAL300000003172 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000003172 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003172/0 /scratch/stefan/7769584/working/building/REAL300000003172 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/194 `/scratch/stefan/7769584/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCN3CCSCC23)C=C1) `REAL300000003172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003172 none O=C([O-])C1=CC=C(N=NC2CCCN3CCSCC23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 10, 5, 5, 14, 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: [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 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 4 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 38, 37]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003172 none O=C([O-])C1=CC=C(N=NC2CCCN3CCSCC23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 10, 5, 5, 14, 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: [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 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003172 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003172/1 /scratch/stefan/7769584/working/building/REAL300000003172 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/195 `/scratch/stefan/7769584/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCC[N@@H+]3CCSCC23)C=C1) `REAL300000003172.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003172 none O=C([O-])C1=CC=C(N=NC2CCC[N@@H+]3CCSCC23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 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: [2, 7, 2, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003172 none O=C([O-])C1=CC=C(N=NC2CCC[N@@H+]3CCSCC23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 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: [2, 7, 2, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003172 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `2' /scratch/stefan/7769584/working/building/REAL300000003172/2 /scratch/stefan/7769584/working/building/REAL300000003172 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 2 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/196 `/scratch/stefan/7769584/working/3D/196' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCC[N@H+]3CCSCC23)C=C1) `REAL300000003172.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000003172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003172/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003172 none O=C([O-])C1=CC=C(N=NC2CCC[N@H+]3CCSCC23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 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: [2, 7, 2, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003172 none O=C([O-])C1=CC=C(N=NC2CCC[N@H+]3CCSCC23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 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: [2, 7, 2, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003172 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003172 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 2: /scratch/stefan/7769584/working/building/REAL300000003172/2.* 1: /scratch/stefan/7769584/working/building/REAL300000003172/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003172/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003172 Building REAL300000003173 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003173' /scratch/stefan/7769584/working/building/REAL300000003173 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003173 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003173/0 /scratch/stefan/7769584/working/building/REAL300000003173 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/197 `/scratch/stefan/7769584/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C3=CC=CC=C3OCC2F)C=C1) `REAL300000003173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003173 none O=C([O-])C1=CC=C(NN=C2C3=CC=CC=C3OCC2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 10, 15, 15, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15] 15 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24, 33]) total number of confs: 66 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: REAL300000003173 none O=C([O-])C1=CC=C(NN=C2C3=CC=CC=C3OCC2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 10, 15, 15, 15, 15, 15, 15, 15, 1, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 31 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003173 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003173 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003173/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003173 Building REAL300000003174 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003174' /scratch/stefan/7769584/working/building/REAL300000003174 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003174 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003174/0 /scratch/stefan/7769584/working/building/REAL300000003174 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/198 `/scratch/stefan/7769584/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCCO3)N=N2)C=C1) `REAL300000003174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003174 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCCO3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 200, 200, 72, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 72, 72, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003174 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCCO3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 49, 66, 66, 48, 48, 8, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 1, 1, 66, 66, 66, 66, 8, 8, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 66, 66] 201 rigid atoms, others: [9, 10, 11, 12, 13, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000003174 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3CCCO3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 23, 68, 68, 68, 163, 201, 201, 201, 201, 68, 68, 1, 1, 1, 1, 23, 23, 68, 163, 163, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003174 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003174 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003174/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003174 Building REAL300000003175 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003175' /scratch/stefan/7769584/working/building/REAL300000003175 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003175 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003175/0 /scratch/stefan/7769584/working/building/REAL300000003175 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/199 `/scratch/stefan/7769584/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(CC=CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300000003175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003175 none CC1=CC(C)=C(CC=CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [66, 62, 76, 76, 76, 61, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 61, 61, 24, 24, 1, 1, 1, 1, 76, 76, 76, 76] 76 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 322 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: REAL300000003175 none CC1=CC(C)=C(CC=CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 72, 72, 76, 76, 72, 72, 76, 76, 76, 76, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 31, 31, 76, 76, 76, 76, 1, 2, 2, 2] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 38] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003175 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003175 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003175/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003175 Building REAL300000003176 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003176' /scratch/stefan/7769584/working/building/REAL300000003176 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003176 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003176/0 /scratch/stefan/7769584/working/building/REAL300000003176 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/200 `/scratch/stefan/7769584/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=N1) `REAL300000003176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003176 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 51, 184, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 51, 184, 201, 201, 201, 201, 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: 478 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003176 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 138, 47, 47, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 138, 201, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 47, 7, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) 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: REAL300000003176 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC(F)=CC=C2F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 138, 138, 88, 138, 138, 138, 138, 138, 1, 1, 11, 11, 11, 9, 11, 11, 11, 1, 2, 2, 2, 1, 13, 72, 138, 138, 138, 138, 11, 9, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 497 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003176 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003176 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003176/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003176 Building REAL300000003177 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003177' /scratch/stefan/7769584/working/building/REAL300000003177 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003177 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003177/0 /scratch/stefan/7769584/working/building/REAL300000003177 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/201 `/scratch/stefan/7769584/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1) `REAL300000003177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003177 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 11, 11, 52, 91, 91, 52, 88, 91, 91, 91, 91, 1, 7, 7, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 52, 91, 91, 91, 91, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7] 91 rigid atoms, others: [34, 35, 36, 37, 38, 33, 39, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41]) total number of confs: 370 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003177 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 23, 43, 43, 23, 38, 43, 43, 43, 43, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 6, 6, 6, 23, 43, 43, 43, 43, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1] 91 rigid atoms, others: [32, 1, 40, 41, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 190 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: REAL300000003177 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 43, 43, 27, 27, 91, 91, 91, 43, 43, 27, 27, 27, 5, 1, 1, 1, 1, 43, 43, 91, 91, 91, 91, 91, 91, 91, 43, 43] 91 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 289 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003177 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003177 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003177/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003177 Building REAL300000003178 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003178' /scratch/stefan/7769584/working/building/REAL300000003178 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003178 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003178/0 /scratch/stefan/7769584/working/building/REAL300000003178 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/202 `/scratch/stefan/7769584/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC(F)=C3N=C2)C=C1) `REAL300000003178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003178 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC(F)=C3N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 30, 38, 38, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 30, 8, 1, 1, 1, 1, 1, 38, 38] 38 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003178 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC(F)=C3N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 9, 22, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 9, 22, 37, 37, 37, 37, 37, 1, 1] 38 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003178 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003178 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003178/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003178 Building REAL300000003179 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003179' /scratch/stefan/7769584/working/building/REAL300000003179 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003179 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003179/0 /scratch/stefan/7769584/working/building/REAL300000003179 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/203 `/scratch/stefan/7769584/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003179 none CN(C)C1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 32, 32, 32, 28, 28, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 6, 1, 1, 1, 1] 32 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 61 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: REAL300000003179 none CN(C)C1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 32, 32, 27, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 1, 1, 1, 8, 27, 32, 32, 32, 32] 32 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 2, 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: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003179 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003179 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003179/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003179 Building REAL300000003180 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003180' /scratch/stefan/7769584/working/building/REAL300000003180 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003180 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003180/0 /scratch/stefan/7769584/working/building/REAL300000003180 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/204 `/scratch/stefan/7769584/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CSC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003180 none CC(C)(C)C1=CSC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 53, 93, 93, 53, 53, 53, 17, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 53, 93, 93, 93, 93, 93, 93, 93, 93, 93, 53, 17, 17, 1, 1, 1, 1] 93 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003180 none CC(C)(C)C1=CSC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 47, 48, 53, 53, 48, 48, 53, 53, 53, 53, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 8, 8, 53, 53, 53, 53] 93 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003180 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003180 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003180/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003180 Building REAL300000003181 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003181' /scratch/stefan/7769584/working/building/REAL300000003181 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003181 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003181/0 /scratch/stefan/7769584/working/building/REAL300000003181 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/205 `/scratch/stefan/7769584/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(CC=CN=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003181 none CC1=CC(C)=C(CC=CN=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 1, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 57 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: REAL300000003181 none CC1=CC(C)=C(CC=CN=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 8, 8, 19, 19, 19, 19, 2, 2, 2, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 55 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003181 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003181 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003181/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003181 Building REAL300000003182 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003182' /scratch/stefan/7769584/working/building/REAL300000003182 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003182 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003182/0 /scratch/stefan/7769584/working/building/REAL300000003182 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/206 `/scratch/stefan/7769584/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003182 none COCCC1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 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, 199, 165, 80, 80, 80, 80, 37, 37, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 80, 201, 201, 201, 199, 199, 165, 165, 80, 37, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003182 none COCCC1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 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, 18, 8, 1, 1, 1, 1, 1, 1, 8, 8, 48, 80, 80, 49, 50, 80, 80, 80, 80, 1, 50, 50, 50, 18, 18, 8, 8, 1, 8, 48, 80, 80, 80, 80] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003182 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003182 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003182/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003182 Building REAL300000003183 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003183' /scratch/stefan/7769584/working/building/REAL300000003183 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003183 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003183/0 /scratch/stefan/7769584/working/building/REAL300000003183 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/207 `/scratch/stefan/7769584/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1S(=O)(=O)N(C)C) `REAL300000003183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003183 none CCC1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1S(=O)(=O)N(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 14, 11, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 104, 104, 104, 104, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 181, 181, 181, 193, 193, 166, 166, 166, 166, 166, 104, 37, 6, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 867 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003183 none CCC1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1S(=O)(=O)N(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 14, 11, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 52, 103, 104, 53, 60, 104, 104, 104, 104, 1, 1, 10, 10, 10, 15, 15, 6, 6, 6, 6, 6, 1, 9, 51, 103, 103, 104, 104, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 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: 531 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003183 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003183 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003183/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003183 Building REAL300000003184 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003184' /scratch/stefan/7769584/working/building/REAL300000003184 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003184 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003184/0 /scratch/stefan/7769584/working/building/REAL300000003184 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/208 `/scratch/stefan/7769584/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br) `REAL300000003184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003184 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 101, 115, 101, 101, 101, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 115, 115, 115, 101, 100, 39, 6, 1, 1, 1, 1, 101] 115 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003184 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 12, 12, 67, 100, 100, 81, 100, 100, 100, 100, 100, 1, 1, 1, 5, 5, 5, 1, 1, 12, 67, 100, 100, 101, 101, 1] 115 rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003184 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003184 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003184/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003184 Building REAL300000003185 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003185' /scratch/stefan/7769584/working/building/REAL300000003185 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003185 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003185/0 /scratch/stefan/7769584/working/building/REAL300000003185 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/209 `/scratch/stefan/7769584/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2[O-])C=C1) `REAL300000003185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003185 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 8, 11, 11, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 8, 4, 1, 1, 11, 11] 11 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003185 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003185 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003185/1 /scratch/stefan/7769584/working/building/REAL300000003185 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/210 `/scratch/stefan/7769584/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2O)C=C1) `REAL300000003185.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003185 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 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: [20, 20, 20, 18, 20, 20, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 18, 6, 1, 1, 2, 20, 20] 40 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 55 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: REAL300000003185 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 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, 9, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 9, 18, 20, 20, 40, 1, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 76 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003185 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003185 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003185/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003185/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003185 Building REAL300000003186 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003186' /scratch/stefan/7769584/working/building/REAL300000003186 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003186 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003186/0 /scratch/stefan/7769584/working/building/REAL300000003186 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/211 `/scratch/stefan/7769584/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2[O-])C=C1) `REAL300000003186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003186 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 8, 11, 11, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 8, 4, 1, 1, 11, 11] 11 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003186 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003186 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003186/1 /scratch/stefan/7769584/working/building/REAL300000003186 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/212 `/scratch/stefan/7769584/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2O)C=C1) `REAL300000003186.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003186 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 18, 6, 1, 1, 2, 23, 23] 46 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28, 29]) 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: REAL300000003186 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 8, 21, 23, 23, 46, 1, 1] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003186 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003186 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003186/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003186/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003186 Building REAL300000003187 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003187' /scratch/stefan/7769584/working/building/REAL300000003187 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003187 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003187/0 /scratch/stefan/7769584/working/building/REAL300000003187 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/213 `/scratch/stefan/7769584/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=C1C) `REAL300000003187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003187 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 27, 41, 41, 32, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2] 41 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003187 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 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, 2, 2, 7, 7, 7, 7, 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: [29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 41, 41, 30, 30, 41, 41, 41, 30, 30, 30, 5, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003187 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003187 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003187/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003187 Building REAL300000003188 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003188' /scratch/stefan/7769584/working/building/REAL300000003188 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003188 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003188/0 /scratch/stefan/7769584/working/building/REAL300000003188 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/214 `/scratch/stefan/7769584/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1) `REAL300000003188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003188 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 28, 67, 67, 188, 201, 201, 188, 188, 201, 201, 201, 201, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 188, 201, 201, 201, 201, 28, 28, 28, 28, 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: 600 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003188 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 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, 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 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, 35, 59, 59, 35, 35, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 28, 28, 28, 7, 7, 7, 35, 59, 59, 59, 59, 1, 1, 1, 1, 28, 28, 28, 28] 201 rigid atoms, others: [1, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19] set([0, 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, 39, 40, 41, 42]) total number of confs: 284 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003188 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 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, 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 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, 1, 1, 20, 59, 59, 43, 59, 59, 59, 114, 201, 201, 201, 201, 201, 201, 20, 20, 20, 4, 1, 1, 1, 1, 59, 59, 59, 59, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 371 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003188 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003188 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003188/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003188 Building REAL300000003189 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003189' /scratch/stefan/7769584/working/building/REAL300000003189 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003189 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003189/0 /scratch/stefan/7769584/working/building/REAL300000003189 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/215 `/scratch/stefan/7769584/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1) `REAL300000003189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003189 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 27, 64, 64, 181, 201, 201, 201, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 181, 201, 201, 201, 201, 27, 27, 27, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 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]) total number of confs: 516 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003189 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 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, 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, 7, 7, 7, 7] 0 hydrogens 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, 8, 36, 65, 65, 36, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 8, 8, 8, 36, 65, 65, 65, 65, 1, 1, 1, 27, 27, 27, 27] 201 rigid atoms, others: [1, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 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, 39, 40, 41, 42]) 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: REAL300000003189 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 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, 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, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 20, 65, 65, 65, 50, 65, 65, 65, 121, 201, 201, 201, 201, 201, 201, 20, 20, 20, 4, 1, 1, 1, 1, 65, 34, 65, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 11, 12, 35] set([0, 1, 2, 9, 10, 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: 379 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003189 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003189 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003189/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003189 Building REAL300000003190 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003190' /scratch/stefan/7769584/working/building/REAL300000003190 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003190 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003190/0 /scratch/stefan/7769584/working/building/REAL300000003190 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/216 `/scratch/stefan/7769584/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCCC3=C2C=NN3CCO)C=C1) `REAL300000003190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003190 none O=C([O-])C1=CC=C(NN=C2CCCC3=C2C=NN3CCO)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 7, 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, 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, 7, 7, 7] 1 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: [16, 6, 16, 6, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 27, 16, 16] 105 rigid atoms, others: [32, 7, 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, 33, 39, 34, 19, 20, 21, 22, 23, 24, 25, 38, 36, 37, 35]) total number of confs: 136 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: REAL300000003190 none O=C([O-])C1=CC=C(NN=C2CCCC3=C2C=NN3CCO)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 7, 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, 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, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 35, 35, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 35, 35, 35, 35, 105, 1, 1] 105 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 24, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 226 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003190 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003190/1 /scratch/stefan/7769584/working/building/REAL300000003190 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/217 `/scratch/stefan/7769584/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCC3=C2C=NN3CCO)C=C1) `REAL300000003190.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003190 none O=C([O-])C1=CC=C(N=NC2CCCC3=C2C=NN3CCO)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 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, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 20, 11, 20, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 36, 20, 20] 102 rigid atoms, others: [32, 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, 6, 7, 39, 34, 19, 20, 21, 22, 23, 24, 36, 33, 38, 37, 35]) 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: REAL300000003190 none O=C([O-])C1=CC=C(N=NC2CCCC3=C2C=NN3CCO)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 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, 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 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, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 34, 34, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 34, 34, 34, 34, 102, 1, 1] 102 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 21, 22, 23, 24, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003190 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003190 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003190/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003190/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003190 Building REAL300000003191 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003191' /scratch/stefan/7769584/working/building/REAL300000003191 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003191 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003191/0 /scratch/stefan/7769584/working/building/REAL300000003191 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/218 `/scratch/stefan/7769584/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1) `REAL300000003191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003191 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 8, 1, 8, 32, 32, 39, 39, 32, 32, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 8, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [2, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003191 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [28, 20, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 39, 39, 39, 39, 39, 28, 28, 28, 28, 28, 20, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [4, 5, 6, 7, 8, 9, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003191 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003191/1 /scratch/stefan/7769584/working/building/REAL300000003191 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/219 `/scratch/stefan/7769584/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1) `REAL300000003191.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003191 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [28, 9, 1, 9, 9, 51, 79, 79, 54, 72, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 29, 28, 28, 28, 28, 51, 79, 79, 80, 80, 1, 1] 91 rigid atoms, others: [2, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 395 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: REAL300000003191 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [54, 33, 33, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 80, 80, 80, 80, 79, 54, 54, 54, 54, 54, 5, 1, 1, 1, 1, 80, 80] 91 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 233 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003191 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003191 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003191/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003191/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003191 Building REAL300000003192 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003192' /scratch/stefan/7769584/working/building/REAL300000003192 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003192 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003192/0 /scratch/stefan/7769584/working/building/REAL300000003192 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/220 `/scratch/stefan/7769584/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)C=C1) `REAL300000003192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003192 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 28, 6, 1, 1, 1, 34, 34] 34 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003192 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 2, 1, 1, 1, 1, 1, 9, 25, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 9, 25, 34, 34, 34, 1, 1] 34 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003192 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003192 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003192/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003192 Building REAL300000003193 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003193' /scratch/stefan/7769584/working/building/REAL300000003193 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003193 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003193/0 /scratch/stefan/7769584/working/building/REAL300000003193 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/221 `/scratch/stefan/7769584/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)C=C1) `REAL300000003193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003193 none O=C([O-])C1=CC=C(NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 24, 27, 27, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 24, 6, 1, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003193 none O=C([O-])C1=CC=C(NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 9, 21, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 21, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003193 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003193 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003193/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003193 Building REAL300000003194 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003194' /scratch/stefan/7769584/working/building/REAL300000003194 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003194 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003194/0 /scratch/stefan/7769584/working/building/REAL300000003194 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/222 `/scratch/stefan/7769584/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1O) `REAL300000003194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003194 none COC1=CC(C)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 27, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 6, 1, 1, 1, 1, 82] 82 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 144 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: REAL300000003194 none COC1=CC(C)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 41, 41, 34, 35, 41, 41, 41, 41, 1, 1, 4, 4, 4, 1, 2, 2, 2, 1, 9, 31, 41, 41, 41, 41, 2] 82 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 143 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003194 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003194 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003194/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003194 Building REAL300000003195 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003195' /scratch/stefan/7769584/working/building/REAL300000003195 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003195 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003195/0 /scratch/stefan/7769584/working/building/REAL300000003195 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/223 `/scratch/stefan/7769584/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)C=C1) `REAL300000003195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003195 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 191, 201, 191, 201, 201, 191, 76, 76, 27, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 191, 76, 27, 27, 27, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 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, 37, 38]) total number of confs: 578 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003195 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [49, 34, 48, 34, 49, 49, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 34, 8, 1, 1, 1, 27, 27, 27, 49, 49] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) 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: REAL300000003195 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 24, 24, 51, 51, 51, 30, 51, 51, 51, 109, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 24, 51, 30, 51, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003195 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003195 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003195/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003195 Building REAL300000003196 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003196' /scratch/stefan/7769584/working/building/REAL300000003196 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003196 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003196/0 /scratch/stefan/7769584/working/building/REAL300000003196 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/224 `/scratch/stefan/7769584/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCOCC1=CC=CC=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003196 none CC(CCOCC1=CC=CC=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 18, 36, 58, 106, 201, 201, 201, 201, 201, 201, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 36, 36, 58, 58, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003196 none CC(CCOCC1=CC=CC=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 75, 52, 15, 3, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 75, 75, 52, 52, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003196 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003196 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003196/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003196 Building REAL300000003197 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003197' /scratch/stefan/7769584/working/building/REAL300000003197 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003197 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003197/0 /scratch/stefan/7769584/working/building/REAL300000003197 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/225 `/scratch/stefan/7769584/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003197 none CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 55, 69, 69, 69, 69, 69, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 93, 93, 93, 69, 69, 69, 27, 27, 27, 7, 1, 1, 1, 1] 93 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 229 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: REAL300000003197 none CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 69, 69, 53, 69, 69, 69, 69, 69, 9, 9, 9, 1, 1, 1, 9, 9, 9, 33, 69, 69, 69, 69] 93 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003197 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003197 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003197/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003197 Building REAL300000003198 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003198' /scratch/stefan/7769584/working/building/REAL300000003198 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003198 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003198/0 /scratch/stefan/7769584/working/building/REAL300000003198 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/226 `/scratch/stefan/7769584/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCCC3=CC=CC=C3C2)C=C1) `REAL300000003198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003198 none O=C([O-])C1=CC=C(N=NC2CCCCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 21, 22, 23, 24]) total number of confs: 7 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: REAL300000003198 none O=C([O-])C1=CC=C(N=NC2CCCCC3=CC=CC=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 16 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003198 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003198 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003198/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003198 Building REAL300000003199 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003199' /scratch/stefan/7769584/working/building/REAL300000003199 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003199 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003199/0 /scratch/stefan/7769584/working/building/REAL300000003199 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/227 `/scratch/stefan/7769584/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NC(C3OCCO3)=CS2)C=C1) `REAL300000003199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003199 none O=C([O-])C1=CC=C(N=NCC2=NC(C3OCCO3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 5, 12, 5, 5, 12, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 201, 201, 201, 75, 13, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 201, 201, 201, 201, 75, 75, 1, 1, 1, 1, 1, 13, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33]) total number of confs: 416 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003199 none O=C([O-])C1=CC=C(N=NCC2=NC(C3OCCO3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 5, 12, 5, 5, 12, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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: [66, 59, 66, 59, 66, 66, 59, 58, 8, 1, 1, 1, 1, 1, 12, 13, 13, 12, 1, 1, 66, 66, 66, 66, 8, 8, 12, 12, 13, 13, 13, 1, 66, 66] 201 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003199 none O=C([O-])C1=CC=C(N=NCC2=NC(C3OCCO3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 5, 12, 5, 5, 12, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 74, 74, 74, 201, 201, 201, 201, 74, 74, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 201, 74, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003199 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003199 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003199/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003199 Building REAL300000003200 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003200' /scratch/stefan/7769584/working/building/REAL300000003200 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003200 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003200/0 /scratch/stefan/7769584/working/building/REAL300000003200 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/228 `/scratch/stefan/7769584/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(CC1=CC=C(F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003200 none CC(C)OCC(CC1=CC=C(F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [175, 146, 175, 85, 27, 4, 27, 66, 71, 71, 66, 71, 71, 71, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 175, 85, 85, 27, 66, 66, 71, 71, 71, 71, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 812 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003200 none CC(C)OCC(CC1=CC=C(F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [109, 79, 109, 30, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 41, 41, 71, 71, 41, 43, 71, 71, 71, 71, 109, 109, 109, 109, 109, 109, 109, 30, 30, 8, 3, 3, 1, 1, 1, 1, 71, 71, 71, 71] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 39, 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, 36, 41, 42, 43, 44]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003200 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003200 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003200/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003200 Building REAL300000003201 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003201' /scratch/stefan/7769584/working/building/REAL300000003201 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003201 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003201/0 /scratch/stefan/7769584/working/building/REAL300000003201 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/229 `/scratch/stefan/7769584/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2NC(=O)C(=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1OC) `REAL300000003201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003201 none COC1=CC=C2NC(=O)C(=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 20, 20, 20, 20, 20, 19, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 20, 20, 19, 6, 1, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003201 none COC1=CC=C2NC(=O)C(=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 19, 19, 20, 20, 20, 20, 1, 1, 1, 5, 4, 4, 4, 1, 1, 1, 7, 20, 20, 20, 20, 5, 5, 5] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003201 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003201 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003201/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003201 Building REAL300000003202 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003202' /scratch/stefan/7769584/working/building/REAL300000003202 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003202 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003202/0 /scratch/stefan/7769584/working/building/REAL300000003202 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/230 `/scratch/stefan/7769584/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCSCC2=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003202 none CN1N=C2CCSCC2=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 14, 5, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 44, 44, 44, 32, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 44, 45, 44, 45, 31, 6, 1, 1, 1, 1] 45 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003202 none CN1N=C2CCSCC2=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 14, 5, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 38, 44, 44, 38, 39, 45, 45, 45, 45, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 37, 44, 44, 45, 45] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003202 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003202 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003202/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003202 Building REAL300000003203 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003203' /scratch/stefan/7769584/working/building/REAL300000003203 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003203 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003203/0 /scratch/stefan/7769584/working/building/REAL300000003203 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/231 `/scratch/stefan/7769584/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1) `REAL300000003203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003203 none CCN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 6, 6, 6, 6, 6, 25, 25, 84, 119, 119, 98, 106, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 6, 25, 84, 119, 119, 119, 119, 1, 1, 1, 1, 1] 155 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: 460 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003203 none CCN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 96, 96, 96, 39, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 119, 119, 96, 119, 119, 96, 154, 154, 154, 154, 154, 96, 39, 6, 1, 1, 1, 1, 119, 119, 116, 119, 119] 155 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003203 none CCN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 12, 12, 52, 96, 96, 60, 74, 96, 96, 96, 96, 1, 1, 6, 6, 1, 6, 6, 1, 9, 9, 9, 9, 9, 1, 12, 52, 96, 96, 96, 96, 6, 6, 1, 6, 6] 155 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003203 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003203 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003203/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003203 Building REAL300000003204 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003204' /scratch/stefan/7769584/working/building/REAL300000003204 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003204 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003204/0 /scratch/stefan/7769584/working/building/REAL300000003204 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/232 `/scratch/stefan/7769584/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C)C=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C) `REAL300000003204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003204 none COCC1=C(C)C=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 73, 73, 47, 47, 73, 73, 73, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 107, 107, 107, 107, 107, 73, 73, 73, 73, 73, 73, 73, 29, 5, 1, 1, 1, 1, 73, 73, 73] 107 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 499 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003204 none COCC1=C(C)C=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 43, 73, 73, 43, 71, 73, 73, 73, 73, 1, 1, 15, 15, 15, 6, 6, 2, 2, 2, 1, 2, 2, 2, 7, 43, 73, 73, 73, 73, 2, 2, 2] 107 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003204 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003204 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003204/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003204 Building REAL300000003205 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003205' /scratch/stefan/7769584/working/building/REAL300000003205 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003205 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003205/0 /scratch/stefan/7769584/working/building/REAL300000003205 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/233 `/scratch/stefan/7769584/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(Cl)=C2)=CC=C1F) `REAL300000003205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003205 none CC1=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 36, 20, 36, 36, 20, 20, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 20, 6, 1, 1, 1, 1, 36, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003205 none CC1=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 8, 1, 1, 1, 1, 1, 1, 4, 4, 18, 36, 36, 18, 36, 36, 36, 36, 36, 1, 1, 1, 37, 37, 15, 36, 37, 37, 37, 37, 1, 1, 4, 18, 36, 36, 36, 36, 1, 37, 37] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 40, 21, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42]) 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: REAL300000003205 none CC1=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 37, 93, 93, 185, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 37, 1, 1, 1, 1, 2, 2, 2, 1, 37, 37, 93, 185, 201, 201, 201, 201, 37, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003205 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003205 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003205/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003205 Building REAL300000003206 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003206' /scratch/stefan/7769584/working/building/REAL300000003206 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003206 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003206/0 /scratch/stefan/7769584/working/building/REAL300000003206 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/234 `/scratch/stefan/7769584/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1) `REAL300000003206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003206 none CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 162, 162, 162, 156, 162, 162, 119, 25, 25, 47, 47, 25, 25, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 47, 201, 201, 201, 201, 201, 162, 162, 162, 162, 47, 47, 25, 6, 1, 1, 1, 1, 47] 201 rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003206 none CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 16, 19, 18, 9, 1, 1, 1, 1, 1, 1, 4, 4, 21, 47, 47, 26, 47, 47, 47, 47, 47, 1, 1, 1, 41, 41, 41, 41, 41, 19, 19, 18, 19, 1, 1, 4, 21, 47, 47, 47, 47, 1] 201 rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 13, 45, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003206 none CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 55, 55, 141, 162, 162, 147, 162, 162, 162, 162, 162, 19, 19, 19, 5, 5, 5, 5, 5, 1, 1, 1, 1, 19, 19, 55, 141, 162, 162, 162, 162, 19] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003206 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003206 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003206/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003206 Building REAL300000003207 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003207' /scratch/stefan/7769584/working/building/REAL300000003207 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003207 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003207/0 /scratch/stefan/7769584/working/building/REAL300000003207 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/235 `/scratch/stefan/7769584/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)C=C1) `REAL300000003207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003207 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 186, 201, 201, 186, 76, 76, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 186, 76, 31, 31, 31, 31, 1, 1, 1, 201, 201] 201 rigid atoms, others: [35, 36, 37, 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, 38, 39]) total number of confs: 575 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003207 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [54, 50, 54, 34, 54, 54, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 31, 31, 54, 54, 54, 54, 33, 8, 1, 1, 1, 1, 31, 31, 31, 54, 54] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) 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: REAL300000003207 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 28, 28, 55, 55, 55, 55, 55, 55, 112, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 28, 55, 55, 55, 55, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003207 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003207 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003207/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003207 Building REAL300000003208 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003208' /scratch/stefan/7769584/working/building/REAL300000003208 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003208 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003208/0 /scratch/stefan/7769584/working/building/REAL300000003208 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/236 `/scratch/stefan/7769584/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003208 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 165, 165, 165, 133, 63, 63, 63, 36, 63, 63, 63, 27, 27, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 165, 165, 165, 165, 165, 165, 63, 37, 63, 27, 6, 1, 1, 1, 1] 165 rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 323 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003208 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 63, 63, 40, 40, 63, 63, 63, 63, 13, 13, 13, 13, 13, 13, 1, 1, 1, 10, 40, 63, 63, 63, 63] 165 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 265 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003208 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 44, 44, 133, 165, 165, 133, 133, 165, 165, 165, 165, 2, 2, 2, 1, 1, 1, 13, 13, 13, 44, 133, 165, 165, 165, 165] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 563 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003208 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003208 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003208/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003208 Building REAL300000003209 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003209' /scratch/stefan/7769584/working/building/REAL300000003209 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003209 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003209/0 /scratch/stefan/7769584/working/building/REAL300000003209 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/237 `/scratch/stefan/7769584/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1F) `REAL300000003209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003209 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 49, 49, 49, 24, 49, 49, 49, 24, 24, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 189, 201, 201, 201, 201, 201, 49, 49, 49, 24, 6, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003209 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 25, 49, 49, 25, 39, 49, 49, 49, 49, 31, 31, 13, 31, 31, 31, 31, 31, 1, 1, 1, 4, 25, 49, 49, 49, 49, 31, 31] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000003209 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 31, 31, 17, 31, 31, 31, 63, 63, 178, 201, 201, 196, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 63, 178, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003209 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003209 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003209/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003209 Building REAL300000003210 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003210' /scratch/stefan/7769584/working/building/REAL300000003210 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003210 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003210/0 /scratch/stefan/7769584/working/building/REAL300000003210 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/238 `/scratch/stefan/7769584/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003210 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', '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, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 168, 168, 168, 135, 50, 50, 50, 30, 50, 50, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 168, 50, 50, 50, 50, 22, 6, 1, 1, 1, 1] 168 rigid atoms, others: [39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 342 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003210 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', '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, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 36, 50, 50, 46, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 9, 36, 50, 50, 50, 50] 168 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003210 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', '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, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 45, 45, 127, 168, 168, 168, 168, 168, 168, 168, 168, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 45, 127, 168, 168, 168, 168] 168 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 400 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003210 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003210 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003210/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003210 Building REAL300000003211 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003211' /scratch/stefan/7769584/working/building/REAL300000003211 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003211 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003211/0 /scratch/stefan/7769584/working/building/REAL300000003211 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/239 `/scratch/stefan/7769584/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)C=C1) `REAL300000003211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003211 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 194, 201, 201, 194, 75, 75, 31, 31, 31, 24, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 194, 75, 31, 31, 31, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003211 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 38, 53, 37, 53, 53, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 31, 53, 53, 53, 53, 37, 10, 1, 1, 1, 31, 31, 31, 31, 53, 53] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) 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: REAL300000003211 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 32, 32, 58, 58, 58, 37, 58, 58, 58, 117, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 10, 32, 58, 33, 58, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003211 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003211 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003211/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003211 Building REAL300000003212 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003212' /scratch/stefan/7769584/working/building/REAL300000003212 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003212 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003212/0 /scratch/stefan/7769584/working/building/REAL300000003212 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/240 `/scratch/stefan/7769584/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003212 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 174, 174, 154, 174, 174, 154, 73, 73, 73, 40, 73, 73, 73, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 174, 154, 174, 174, 73, 73, 73, 32, 7, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 628 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003212 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 11, 11, 11, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 41, 73, 73, 42, 45, 73, 73, 73, 73, 22, 22, 22, 22, 22, 11, 6, 11, 11, 1, 1, 1, 11, 41, 73, 73, 73, 73] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 393 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003212 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 33, 33, 130, 174, 174, 132, 146, 174, 174, 174, 174, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 11, 33, 130, 174, 174, 174, 174] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 614 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003212 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003212 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003212/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003212 Building REAL300000003213 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003213' /scratch/stefan/7769584/working/building/REAL300000003213 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003213 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003213/0 /scratch/stefan/7769584/working/building/REAL300000003213 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/241 `/scratch/stefan/7769584/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003213 none CC1=C(Br)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 2, 2, 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, 26, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 34, 25, 6, 1, 1, 1, 1] 35 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24]) 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: REAL300000003213 none CC1=C(Br)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 2, 2, 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, 10, 10, 28, 34, 34, 28, 28, 34, 34, 34, 34, 1, 2, 2, 2, 1, 10, 28, 34, 34, 35, 34] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 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/7769584/working/building/REAL300000003213 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003213 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003213/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003213 Building REAL300000003214 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003214' /scratch/stefan/7769584/working/building/REAL300000003214 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003214 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003214/0 /scratch/stefan/7769584/working/building/REAL300000003214 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/242 `/scratch/stefan/7769584/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1OC)C(=NNC1=CC=C(C(=O)[O-])C=C1)CCCC2) `REAL300000003214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003214 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=C(C(=O)[O-])C=C1)CCCC2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 27, 27, 27, 27, 27, 27, 27, 39, 27, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 39, 39, 39, 27, 27, 39, 39, 39, 6, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27] 39 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003214 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=C(C(=O)[O-])C=C1)CCCC2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 8, 27, 27, 8, 12, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 4, 1, 1, 4, 4, 4, 8, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 22, 23, 24, 25, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003214 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003214 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003214/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003214 Building REAL300000003215 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003215' /scratch/stefan/7769584/working/building/REAL300000003215 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003215 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003215/0 /scratch/stefan/7769584/working/building/REAL300000003215 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/243 `/scratch/stefan/7769584/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1) `REAL300000003215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003215 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 105, 85, 21, 21, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 105, 105, 105, 105, 85, 21, 3, 3, 3, 1, 1, 1, 1, 3, 105, 105] 105 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 239 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003215 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 80, 105, 105, 62, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 105, 105, 105, 105, 62, 12, 1, 1, 1, 3, 3, 3, 3, 1, 105, 105] 105 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37, 38]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003215 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 39, 39, 104, 104, 104, 104, 104, 105, 105, 104, 104, 105, 105, 104, 1, 1, 1, 1, 9, 39, 104, 104, 104, 105, 105, 105, 105, 104, 1, 1] 105 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003215 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003215 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003215/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003215 Building REAL300000003216 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003216' /scratch/stefan/7769584/working/building/REAL300000003216 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003216 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003216/0 /scratch/stefan/7769584/working/building/REAL300000003216 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/244 `/scratch/stefan/7769584/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2I)C=C1) `REAL300000003216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003216 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2I)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 18, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 30, 27, 30, 30, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 27, 9, 1, 1, 1, 30, 30] 30 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003216 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2I)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 18, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 24, 24, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 12, 24, 30, 30, 30, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003216 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003216 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003216/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003216 Building REAL300000003217 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003217' /scratch/stefan/7769584/working/building/REAL300000003217 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003217 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003217/0 /scratch/stefan/7769584/working/building/REAL300000003217 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/245 `/scratch/stefan/7769584/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300000003217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003217 none CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 77, 77, 77, 77, 23, 23, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 77, 77, 77, 201, 201, 201, 201, 201, 201, 201, 77, 77, 23, 6, 1, 1, 1, 1, 77, 77, 77, 77] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003217 none CCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 31, 7, 1, 1, 1, 1, 1, 1, 6, 6, 44, 77, 77, 46, 59, 77, 77, 77, 77, 1, 1, 1, 55, 55, 55, 54, 54, 31, 31, 1, 1, 6, 44, 77, 77, 77, 77, 1, 2, 2, 2] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 22, 38, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003217 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003217 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003217/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003217 Building REAL300000003218 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003218' /scratch/stefan/7769584/working/building/REAL300000003218 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003218 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003218/0 /scratch/stefan/7769584/working/building/REAL300000003218 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/246 `/scratch/stefan/7769584/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1COC1=CC=CC=C1) `REAL300000003218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003218 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1COC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 14, 14, 14, 14, 14, 14, 47, 47, 161, 201, 201, 161, 188, 201, 201, 201, 201, 14, 6, 2, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 14, 14, 47, 161, 201, 201, 201, 201, 14, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 701 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003218 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1COC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 26, 26, 72, 72, 26, 26, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 72, 72, 72, 197, 201, 201, 201, 201, 201, 201, 90, 90, 90, 72, 72, 26, 6, 1, 1, 1, 1, 72, 197, 197, 201, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 781 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: REAL300000003218 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1COC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 39, 72, 72, 40, 62, 72, 72, 72, 72, 1, 1, 1, 7, 13, 14, 14, 13, 14, 14, 3, 3, 3, 1, 1, 6, 39, 72, 72, 72, 72, 1, 7, 7, 14, 14, 13, 14, 14] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 39, 18, 19, 20, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003218 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003218 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003218/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003218 Building REAL300000003219 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003219' /scratch/stefan/7769584/working/building/REAL300000003219 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003219 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003219/0 /scratch/stefan/7769584/working/building/REAL300000003219 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/247 `/scratch/stefan/7769584/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1CN1C=CC=N1) `REAL300000003219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003219 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 87, 87, 195, 201, 201, 199, 201, 201, 201, 201, 201, 29, 9, 1, 1, 1, 1, 1, 1, 47, 47, 47, 29, 29, 87, 195, 201, 201, 201, 201, 29, 9, 9, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 578 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003219 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 42, 42, 21, 21, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 42, 42, 100, 201, 201, 201, 201, 56, 56, 56, 42, 42, 21, 5, 1, 1, 1, 1, 42, 100, 100, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003219 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 8, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 42, 42, 28, 42, 42, 42, 42, 42, 1, 1, 1, 8, 29, 29, 29, 29, 3, 3, 3, 1, 1, 6, 27, 42, 42, 42, 42, 1, 8, 8, 29, 29, 29] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 29, 30, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003219 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003219 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003219/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003219 Building REAL300000003220 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003220' /scratch/stefan/7769584/working/building/REAL300000003220 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003220 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003220/0 /scratch/stefan/7769584/working/building/REAL300000003220 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/248 `/scratch/stefan/7769584/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003220 none CCOC1=CC=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 150, 150, 151, 55, 151, 151, 151, 35, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 150, 151, 35, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003220 none CCOC1=CC=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 91, 150, 150, 102, 150, 150, 150, 150, 150, 33, 33, 33, 33, 33, 1, 1, 1, 12, 91, 149, 150, 150, 150] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003220 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003220 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003220/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003220 Building REAL300000003221 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003221' /scratch/stefan/7769584/working/building/REAL300000003221 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003221 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003221/0 /scratch/stefan/7769584/working/building/REAL300000003221 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/249 `/scratch/stefan/7769584/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003221 none CC1=CC=C(Br)C(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 50, 50, 50, 50, 50, 25, 7, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003221 none CC1=CC=C(Br)C(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 50, 50, 44, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 12, 44, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003221 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003221 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003221/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003221 Building REAL300000003222 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003222' /scratch/stefan/7769584/working/building/REAL300000003222 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003222 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003222/0 /scratch/stefan/7769584/working/building/REAL300000003222 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/250 `/scratch/stefan/7769584/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003222 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 142, 145, 145, 115, 56, 56, 56, 33, 56, 56, 56, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 145, 145, 145, 56, 56, 56, 28, 6, 1, 1, 1, 1, 145, 145, 145, 145] 145 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 337 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003222 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 12, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 56, 56, 35, 40, 56, 56, 56, 56, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 35, 56, 56, 56, 56, 13, 13, 13, 13] 145 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003222 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 41, 41, 116, 145, 145, 116, 145, 145, 145, 145, 145, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13, 41, 116, 145, 145, 145, 145, 2, 2, 2, 1] 145 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 462 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003222 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003222 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003222/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003222 Building REAL300000003223 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003223' /scratch/stefan/7769584/working/building/REAL300000003223 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003223 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003223/0 /scratch/stefan/7769584/working/building/REAL300000003223 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/251 `/scratch/stefan/7769584/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003223 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 32, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 32, 7, 1, 1, 1, 1] 49 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003223 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 9, 9, 41, 49, 49, 46, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 2, 2, 2, 9, 41, 49, 49, 49, 49] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 26, 27] set([6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003223 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003223 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003223/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003223 Building REAL300000003224 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003224' /scratch/stefan/7769584/working/building/REAL300000003224 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003224 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003224/0 /scratch/stefan/7769584/working/building/REAL300000003224 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/252 `/scratch/stefan/7769584/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1) `REAL300000003224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003224 none O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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: [2, 7, 2, 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, 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, 22, 23, 23, 22, 22, 9, 9, 9, 9, 9, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 9, 9, 23, 23] 23 rigid atoms, others: [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, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003224 none O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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: [2, 7, 2, 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, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 8, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 8, 9, 9, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 1, 1, 13, 13] 23 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 76 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003224 none O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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: [2, 7, 2, 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, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 13, 13, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 48, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003224 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003224/1 /scratch/stefan/7769584/working/building/REAL300000003224 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/253 `/scratch/stefan/7769584/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1) `REAL300000003224.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003224 none O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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: [2, 7, 2, 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, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 18, 19, 19, 18, 18, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 1, 9, 9, 19, 19] 19 rigid atoms, others: [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, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003224 none O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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: [2, 7, 2, 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, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 8, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 7, 9, 9, 1, 1, 1, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 7, 9, 9, 1, 1, 14, 14] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003224 none O=C([O-])C1=CC=C(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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: [2, 7, 2, 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, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 15, 15, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 48, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003224 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003224 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003224/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003224/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003224 Building REAL300000003225 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003225' /scratch/stefan/7769584/working/building/REAL300000003225 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003225 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003225/0 /scratch/stefan/7769584/working/building/REAL300000003225 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/254 `/scratch/stefan/7769584/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003225 none COC(=O)C1=C(C)NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 52, 72, 52, 52, 52, 52, 33, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 72, 72, 72, 52, 52, 52, 52, 32, 6, 1, 1, 1, 1, 52] 72 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003225 none COC(=O)C1=C(C)NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 35, 51, 51, 35, 35, 51, 51, 51, 51, 1, 13, 13, 13, 2, 2, 2, 1, 6, 35, 51, 52, 52, 52, 1] 72 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 21, 28] set([0, 1, 3, 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: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003225 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003225 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003225/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003225 Building REAL300000003226 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003226' /scratch/stefan/7769584/working/building/REAL300000003226 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003226 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003226/0 /scratch/stefan/7769584/working/building/REAL300000003226 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/255 `/scratch/stefan/7769584/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1[N+](=O)[O-]) `REAL300000003226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003226 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(F)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 19, 19, 14, 14, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 14, 19, 19, 19, 19, 1, 1, 1] 19 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003226 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(F)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 6, 1, 1, 1, 1, 19, 19, 19] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 37 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003226 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003226/1 /scratch/stefan/7769584/working/building/REAL300000003226 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/256 `/scratch/stefan/7769584/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1[N+](=O)[O-]) `REAL300000003226.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003226 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003226 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 11, 11, 11, 9, 11, 11, 11, 11, 11, 9, 9, 9, 9, 1, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003226 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003226 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003226/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003226/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003226 Building REAL300000003227 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003227' /scratch/stefan/7769584/working/building/REAL300000003227 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003227 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003227/0 /scratch/stefan/7769584/working/building/REAL300000003227 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/257 `/scratch/stefan/7769584/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003227 none NS(=O)(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 67, 138, 138, 67, 59, 67, 67, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 138, 138, 64, 67, 67, 37, 6, 1, 1, 1, 1, 67] 138 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 488 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003227 none NS(=O)(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 48, 67, 67, 48, 66, 67, 67, 67, 67, 1, 5, 5, 1, 1, 1, 9, 48, 67, 67, 67, 67, 1] 138 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 21, 24, 25, 26] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31, 32]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003227 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003227 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003227/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003227 Building REAL300000003228 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003228' /scratch/stefan/7769584/working/building/REAL300000003228 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003228 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003228/0 /scratch/stefan/7769584/working/building/REAL300000003228 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/258 `/scratch/stefan/7769584/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CN2C=C(CN=NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1) `REAL300000003228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003228 none COC1=CC=C(CN2C=C(CN=NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 178, 201, 201, 176, 52, 52, 52, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 176, 176, 52, 18, 18, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 750 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003228 none COC1=CC=C(CN2C=C(CN=NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 9, 27, 27, 8, 1, 1, 1, 1, 1, 6, 40, 40, 52, 52, 40, 40, 52, 52, 52, 52, 1, 1, 27, 27, 27, 27, 27, 27, 27, 8, 8, 1, 6, 6, 52, 52, 52, 52, 27, 27] 201 rigid atoms, others: [33, 6, 7, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 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, 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: REAL300000003228 none COC1=CC=C(CN2C=C(CN=NC3=CC=C(C(=O)[O-])C=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 79, 79, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003228 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003228 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003228/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003228 Building REAL300000003229 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003229' /scratch/stefan/7769584/working/building/REAL300000003229 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003229 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003229/0 /scratch/stefan/7769584/working/building/REAL300000003229 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/259 `/scratch/stefan/7769584/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NN2CCCC(=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1) `REAL300000003229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003229 none COC(=O)C1=NN2CCCC(=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 9, 21, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 21, 21, 21, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 9] 21 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 58 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: REAL300000003229 none COC(=O)C1=NN2CCCC(=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 1] 21 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38, 22, 23, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 28 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003229 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003229 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003229/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003229 Building REAL300000003230 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003230' /scratch/stefan/7769584/working/building/REAL300000003230 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003230 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003230/0 /scratch/stefan/7769584/working/building/REAL300000003230 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/260 `/scratch/stefan/7769584/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(F)=C1) `REAL300000003230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003230 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(F)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 37, 55, 37, 37, 37, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 55, 55, 55, 37, 37, 25, 5, 1, 1, 1, 1, 37] 55 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003230 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(F)=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 9, 9, 31, 37, 37, 31, 31, 37, 37, 37, 37, 1, 1, 1, 8, 8, 8, 1, 1, 9, 31, 37, 37, 37, 37, 1] 55 rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003230 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003230 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003230/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003230 Building REAL300000003231 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003231' /scratch/stefan/7769584/working/building/REAL300000003231 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003231 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003231/0 /scratch/stefan/7769584/working/building/REAL300000003231 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/261 `/scratch/stefan/7769584/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1) `REAL300000003231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003231 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 199, 201, 201, 199, 89, 89, 31, 31, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 31, 201, 201, 201, 201, 199, 89, 31, 31, 31, 1, 1, 1, 1, 31, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003231 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 29, 41, 29, 41, 41, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 1, 41, 41, 41, 41, 28, 6, 1, 1, 1, 31, 31, 31, 31, 1, 41, 41] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37, 38]) 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: REAL300000003231 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 15, 15, 44, 44, 44, 44, 44, 134, 201, 201, 201, 201, 201, 44, 1, 1, 1, 1, 4, 15, 44, 44, 44, 201, 201, 201, 201, 44, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003231 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003231 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003231/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003231 Building REAL300000003232 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003232' /scratch/stefan/7769584/working/building/REAL300000003232 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003232 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003232/0 /scratch/stefan/7769584/working/building/REAL300000003232 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/262 `/scratch/stefan/7769584/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1) `REAL300000003232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003232 none COC1=CC=CC(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 67, 65, 24, 24, 65, 65, 24, 24, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 67, 67, 65, 65, 24, 6, 1, 1, 1, 1, 65, 65, 201] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 415 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003232 none COC1=CC=CC(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 16, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 42, 65, 65, 42, 44, 65, 65, 65, 65, 1, 1, 17, 25, 25, 25, 16, 17, 17, 3, 3, 1, 1, 6, 42, 65, 65, 65, 65, 1, 1, 17] 201 rigid atoms, others: [45, 36, 37, 7, 8, 9, 10, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 311 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: REAL300000003232 none COC1=CC=CC(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 17, 17, 17, 17, 17, 55, 55, 176, 201, 201, 176, 191, 201, 201, 201, 201, 17, 17, 1, 3, 3, 3, 1, 1, 1, 9, 9, 17, 17, 55, 176, 201, 201, 201, 201, 16, 17, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 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, 45]) total number of confs: 634 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003232 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003232 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003232/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003232 Building REAL300000003233 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003233' /scratch/stefan/7769584/working/building/REAL300000003233 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003233 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003233/0 /scratch/stefan/7769584/working/building/REAL300000003233 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/263 `/scratch/stefan/7769584/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1) `REAL300000003233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003233 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need 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, 201, 180, 201, 201, 180, 59, 59, 19, 19, 19, 19, 19, 6, 2, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 180, 59, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 19, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 653 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003233 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens 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, 52, 87, 52, 87, 87, 52, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 18, 19, 19, 19, 19, 19, 1, 87, 87, 87, 87, 52, 6, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 1, 88, 88] 201 rigid atoms, others: [32, 40, 9, 10, 11, 12, 13, 14, 15, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 386 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: REAL300000003233 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 34, 35, 91, 91, 35, 91, 91, 190, 201, 201, 201, 201, 201, 201, 91, 1, 1, 1, 1, 10, 34, 91, 91, 35, 190, 190, 201, 201, 201, 201, 201, 90, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 701 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003233 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003233 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003233/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003233 Building REAL300000003234 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003234' /scratch/stefan/7769584/working/building/REAL300000003234 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003234 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003234/0 /scratch/stefan/7769584/working/building/REAL300000003234 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/264 `/scratch/stefan/7769584/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1) `REAL300000003234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003234 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 7, 7, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 25, 25, 25, 25, 17, 7, 3, 3, 1, 1, 1, 1, 3, 3, 25, 25] 25 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 71 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003234 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 12, 18, 18, 9, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 3, 1, 1, 18, 18, 18, 18, 9, 3, 1, 1, 3, 3, 3, 3, 1, 1, 18, 18] 25 rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) total number of confs: 68 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003234 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 25, 25, 17, 18, 25, 25, 25, 25, 17, 17, 1, 1, 1, 1, 5, 17, 17, 17, 25, 25, 25, 25, 17, 17, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003234 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003234 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003234/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003234 Building REAL300000003235 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003235' /scratch/stefan/7769584/working/building/REAL300000003235 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003235 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003235/0 /scratch/stefan/7769584/working/building/REAL300000003235 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/265 `/scratch/stefan/7769584/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC(F)F)C=C1) `REAL300000003235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003235 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [50, 50, 50, 26, 50, 50, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 104, 104, 50, 50, 50, 50, 26, 6, 1, 1, 1, 1, 39, 39, 104, 50, 50] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003235 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 27, 27, 57, 57, 28, 57, 57, 57, 132, 199, 201, 201, 1, 1, 1, 1, 7, 27, 57, 57, 57, 57, 199, 199, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003235 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003235 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003235/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003235 Building REAL300000003236 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003236' /scratch/stefan/7769584/working/building/REAL300000003236 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003236 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003236/0 /scratch/stefan/7769584/working/building/REAL300000003236 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/266 `/scratch/stefan/7769584/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=C(F)C=C3N2)C=C1) `REAL300000003236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003236 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=C(F)C=C3N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 26, 21, 26, 26, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 27, 27, 21, 6, 1, 1, 1, 1, 26, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003236 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=C(F)C=C3N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 1, 1, 1, 1, 8, 22, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003236 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003236 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003236/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003236 Building REAL300000003237 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003237' /scratch/stefan/7769584/working/building/REAL300000003237 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003237 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003237/0 /scratch/stefan/7769584/working/building/REAL300000003237 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/267 `/scratch/stefan/7769584/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1) `REAL300000003237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003237 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 14, 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, 2, 2, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 72, 72, 146, 160, 160, 160, 160, 160, 160, 160, 160, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 71, 146, 160, 160, 160, 160, 1, 1, 1] 160 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003237 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 14, 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, 2, 2, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 96, 96, 96, 160, 160, 160, 160, 96, 96, 96, 96, 40, 7, 1, 1, 1, 1, 160, 160, 160] 160 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000003237 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CS2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 14, 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, 2, 2, 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 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, 13, 13, 66, 96, 96, 77, 96, 96, 96, 96, 96, 1, 1, 1, 13, 13, 13, 13, 1, 2, 2, 2, 13, 66, 96, 96, 96, 96, 13, 13, 13] 160 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003237 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003237 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003237/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003237 Building REAL300000003238 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003238' /scratch/stefan/7769584/working/building/REAL300000003238 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003238 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003238/0 /scratch/stefan/7769584/working/building/REAL300000003238 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/268 `/scratch/stefan/7769584/working/3D/268' -> `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(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003238 none COC(=O)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 71, 119, 39, 90, 90, 38, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 119, 119, 119, 90, 90, 38, 38, 38, 6, 1, 1, 1, 1, 90, 90, 90, 90] 119 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 453 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003238 none COC(=O)C1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 8, 48, 90, 90, 48, 54, 90, 90, 90, 90, 1, 1, 1, 13, 13, 13, 1, 1, 8, 8, 8, 48, 90, 90, 90, 90, 2, 2, 2, 1] 119 rigid atoms, others: [2, 4, 5, 6, 7, 8, 40, 21, 22, 23, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 451 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003238 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003238 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003238/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003238 Building REAL300000003239 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003239' /scratch/stefan/7769584/working/building/REAL300000003239 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003239 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003239/0 /scratch/stefan/7769584/working/building/REAL300000003239 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/269 `/scratch/stefan/7769584/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1) `REAL300000003239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003239 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [33, 7, 33, 33, 100, 152, 152, 100, 152, 152, 152, 152, 152, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 100, 152, 152, 152, 152, 6, 7, 7, 1, 1, 1, 7] 152 rigid atoms, others: [35, 36, 37, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 567 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003239 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 47, 78, 78, 47, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 12, 12, 12, 47, 78, 78, 78, 78, 1, 1, 1, 7, 7, 7, 1] 152 rigid atoms, others: [32, 1, 34, 38, 33, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 323 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: REAL300000003239 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 78, 78, 78, 78, 78, 152, 152, 152, 152, 78, 31, 31, 31, 6, 1, 1, 1, 1, 78, 78, 78, 152, 152, 152, 78] 152 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 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: 266 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003239 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003239 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003239/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003239 Building REAL300000003240 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003240' /scratch/stefan/7769584/working/building/REAL300000003240 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003240 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003240/0 /scratch/stefan/7769584/working/building/REAL300000003240 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/270 `/scratch/stefan/7769584/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1) `REAL300000003240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003240 none O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 95, 41, 95, 95, 41, 7, 7, 1, 7, 49, 64, 86, 86, 64, 86, 86, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 41, 49, 49, 64, 64, 86, 86, 64, 86, 86, 1, 1, 1, 1, 95, 95] 201 rigid atoms, others: [38, 39, 40, 9, 41, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 785 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003240 none O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 103, 146, 103, 146, 146, 103, 29, 29, 7, 3, 1, 1, 1, 1, 1, 1, 1, 29, 86, 86, 86, 86, 86, 146, 146, 146, 146, 103, 7, 7, 3, 3, 1, 1, 1, 1, 1, 86, 86, 86, 86, 146, 146] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39, 40, 41, 42, 43]) total number of confs: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003240 none O=C([O-])C1=CC=C(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 116, 138, 149, 149, 138, 149, 149, 32, 100, 100, 100, 100, 100, 1, 1, 1, 1, 7, 116, 116, 138, 138, 149, 149, 138, 149, 149, 100, 100, 100, 100, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 43, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 658 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003240 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003240 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003240/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003240 Building REAL300000003241 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003241' /scratch/stefan/7769584/working/building/REAL300000003241 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003241 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003241/0 /scratch/stefan/7769584/working/building/REAL300000003241 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/271 `/scratch/stefan/7769584/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1) `REAL300000003241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003241 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7] 0 hydrogens 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, 15, 57, 57, 170, 201, 201, 170, 170, 201, 201, 201, 201, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 170, 201, 201, 201, 201, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 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]) total number of confs: 676 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003241 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7] 0 hydrogens 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, 110, 110, 58, 58, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 10, 10, 10, 58, 110, 110, 110, 110, 1, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [1, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 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, 39, 40, 41, 42]) total number of confs: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003241 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 32, 110, 110, 110, 75, 110, 110, 110, 192, 201, 201, 201, 201, 201, 201, 32, 32, 32, 6, 1, 1, 1, 1, 110, 75, 110, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 11, 12, 35] set([0, 1, 2, 9, 10, 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: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003241 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003241 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003241/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003241 Building REAL300000003242 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003242' /scratch/stefan/7769584/working/building/REAL300000003242 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003242 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003242/0 /scratch/stefan/7769584/working/building/REAL300000003242 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/272 `/scratch/stefan/7769584/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1) `REAL300000003242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003242 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 25, 41, 41, 26, 26, 42, 42, 42, 42, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 12, 12, 25, 41, 41, 42, 42, 1, 1] 42 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003242 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 42, 42, 42, 42, 42, 42, 42, 41, 28, 28, 28, 5, 1, 1, 1, 1, 42, 42] 42 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/7769584/working/building/REAL300000003242 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003242/1 /scratch/stefan/7769584/working/building/REAL300000003242 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/273 `/scratch/stefan/7769584/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1) `REAL300000003242.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003242 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [13, 1, 13, 39, 39, 42, 42, 39, 39, 42, 42, 42, 42, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 42, 42, 42, 42, 1, 1] 42 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003242 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 42, 42, 42, 42, 42, 42, 42, 42, 21, 21, 21, 21, 1, 1, 1, 1, 42, 42] 42 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003242 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003242 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003242/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003242/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003242 Building REAL300000003243 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003243' /scratch/stefan/7769584/working/building/REAL300000003243 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003243 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003243/0 /scratch/stefan/7769584/working/building/REAL300000003243 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/274 `/scratch/stefan/7769584/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1) `REAL300000003243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003243 none COC(=O)C1=CC(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 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, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 26, 38, 26, 26, 16, 5, 16, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 26, 26, 38, 38, 38, 26, 16, 16, 16, 16, 1, 1, 1, 1] 38 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000003243 none COC(=O)C1=CC(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 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, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 5, 5, 21, 21, 26, 26, 21, 22, 26, 26, 26, 26, 1, 1, 1, 1, 1, 7, 7, 7, 1, 5, 5, 5, 5, 26, 26, 26, 26] 38 rigid atoms, others: [2, 4, 5, 6, 7, 20, 21, 22, 23, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003243 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003243/1 /scratch/stefan/7769584/working/building/REAL300000003243 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/275 `/scratch/stefan/7769584/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1) `REAL300000003243.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003243 none COC(=O)C1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 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, 4, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 39, 49, 39, 39, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 49, 49, 49, 39, 22, 22, 22, 6, 1, 1, 1, 1] 49 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 101 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: REAL300000003243 none COC(=O)C1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 8, 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, 4, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 7, 7, 7, 25, 39, 39, 25, 25, 39, 39, 39, 39, 1, 1, 2, 2, 1, 11, 11, 11, 1, 7, 7, 7, 25, 39, 39, 39, 39] 49 rigid atoms, others: [2, 4, 5, 6, 7, 20, 21, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003243 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003243 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003243/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003243/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003243 Building REAL300000003244 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003244' /scratch/stefan/7769584/working/building/REAL300000003244 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003244 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003244/0 /scratch/stefan/7769584/working/building/REAL300000003244 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/276 `/scratch/stefan/7769584/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Br)N=C3COCCN32)C=C1) `REAL300000003244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003244 none O=C([O-])C1=CC=C(NN=CC2=C(Br)N=C3COCCN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 15, 5, 1, 1, 1, 1, 1, 1, 20, 20] 20 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 33]) 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: REAL300000003244 none O=C([O-])C1=CC=C(NN=CC2=C(Br)N=C3COCCN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 9, 19, 20, 20, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003244 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003244 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003244/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003244 Building REAL300000003245 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003245' /scratch/stefan/7769584/working/building/REAL300000003245 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003245 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003245/0 /scratch/stefan/7769584/working/building/REAL300000003245 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/277 `/scratch/stefan/7769584/working/3D/277' -> `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(C(=O)[O-])C=C2)N1) `REAL300000003245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003245 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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: [119, 73, 73, 73, 73, 130, 130, 130, 73, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 119, 119, 119, 119, 119, 130, 130, 130, 73, 39, 6, 1, 1, 1, 1, 72] 148 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003245 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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: [6, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 6, 6, 36, 72, 73, 36, 36, 73, 73, 73, 73, 1, 6, 6, 6, 6, 6, 12, 12, 12, 1, 6, 35, 72, 72, 73, 73, 1] 148 rigid atoms, others: [1, 2, 3, 4, 38, 8, 9, 10, 22, 31] set([0, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003245 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003245 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003245/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003245 Building REAL300000003246 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003246' /scratch/stefan/7769584/working/building/REAL300000003246 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003246 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003246/0 /scratch/stefan/7769584/working/building/REAL300000003246 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/278 `/scratch/stefan/7769584/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CN(C(=O)OC(C)(C)C)C1) `REAL300000003246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003246 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CN(C(=O)OC(C)(C)C)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [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, 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: [12, 7, 1, 7, 34, 34, 55, 55, 34, 34, 55, 55, 55, 55, 1, 1, 1, 1, 7, 7, 18, 23, 23, 23, 1, 12, 12, 12, 12, 12, 7, 55, 55, 55, 55, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 149 rigid atoms, others: [48, 2, 35, 36, 37, 14, 15, 16, 17, 24, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 309 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: REAL300000003246 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CN(C(=O)OC(C)(C)C)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [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, 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: [30, 25, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 55, 55, 55, 94, 94, 145, 149, 149, 149, 55, 40, 40, 40, 40, 40, 25, 1, 1, 1, 1, 55, 55, 55, 149, 149, 149, 149, 149, 149, 149, 149, 149, 55, 55] 149 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 12, 13, 31] set([0, 1, 2, 3, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 561 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003246 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003246 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003246/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003246 Building REAL300000003247 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003247' /scratch/stefan/7769584/working/building/REAL300000003247 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003247 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003247/0 /scratch/stefan/7769584/working/building/REAL300000003247 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/279 `/scratch/stefan/7769584/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CN=C2)=N1) `REAL300000003247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003247 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 125, 125, 23, 125, 5, 5, 5, 5, 5, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 5, 174, 174, 174, 174, 174, 23, 23, 5, 7, 18, 18, 18, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 628 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003247 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 96, 96, 25, 96, 9, 9, 9, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 9, 119, 119, 119, 119, 119, 25, 25, 9, 7, 4, 1, 1, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003247 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 41, 41, 8, 41, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 5, 5, 1, 65, 65, 65, 65, 65, 8, 8, 1, 4, 9, 9, 9, 9, 9, 5, 5, 5, 5] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 21, 22, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003247 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003247 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003247/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003247 Building REAL300000003248 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003248' /scratch/stefan/7769584/working/building/REAL300000003248 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003248 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003248/0 /scratch/stefan/7769584/working/building/REAL300000003248 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/280 `/scratch/stefan/7769584/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CN(C)N=C2)=N1) `REAL300000003248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003248 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CN(C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 125, 27, 125, 9, 9, 9, 9, 9, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 9, 150, 150, 150, 150, 150, 27, 27, 9, 11, 24, 24, 24, 24, 24, 1, 2, 2, 2, 1] 201 rigid atoms, others: [43, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 530 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003248 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CN(C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 147, 147, 40, 147, 14, 14, 14, 8, 8, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 24, 24, 24, 24, 24, 14, 161, 161, 161, 161, 161, 40, 40, 14, 8, 6, 1, 1, 1, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003248 none CCOC(=O)CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CN(C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 6, 39, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 9, 9, 9, 9, 9, 1, 56, 56, 56, 56, 56, 6, 6, 1, 4, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 21, 22, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003248 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003248 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003248/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003248 Building REAL300000003249 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003249' /scratch/stefan/7769584/working/building/REAL300000003249 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003249 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003249/0 /scratch/stefan/7769584/working/building/REAL300000003249 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/281 `/scratch/stefan/7769584/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CC1CN(C(=O)OC(C)(C)C)C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003249 none CC(C)C(CC1CN(C(=O)OC(C)(C)C)C1)N=NC1=CC=C(C(=O)[O-])C=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 41, 5, 20, 37, 71, 71, 71, 97, 97, 156, 157, 157, 157, 71, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 45, 45, 45, 45, 45, 20, 39, 39, 71, 71, 71, 157, 157, 157, 157, 157, 157, 157, 157, 157, 71, 71, 1, 1, 1, 1] 201 rigid atoms, others: [51, 54, 17, 18, 19, 20, 21, 22, 25, 52, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 590 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003249 none CC(C)C(CC1CN(C(=O)OC(C)(C)C)C1)N=NC1=CC=C(C(=O)[O-])C=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 40, 6, 1, 1, 1, 1, 1, 4, 4, 10, 13, 13, 13, 1, 17, 46, 46, 71, 71, 46, 46, 71, 71, 71, 71, 41, 41, 40, 41, 41, 40, 41, 17, 6, 6, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 71, 71, 71, 71] 201 rigid atoms, others: [4, 37, 6, 7, 8, 39, 15, 49, 50, 38, 5] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003249 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003249 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003249/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003249 Building REAL300000003250 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003250' /scratch/stefan/7769584/working/building/REAL300000003250 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003250 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003250/0 /scratch/stefan/7769584/working/building/REAL300000003250 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/282 `/scratch/stefan/7769584/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)C=C1) `REAL300000003250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003250 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 201, 201, 187, 68, 68, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 187, 68, 20, 20, 20, 1, 1, 1, 201, 201] 201 rigid atoms, others: [35, 36, 37, 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, 38, 39]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003250 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [70, 70, 70, 55, 70, 70, 51, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 8, 18, 18, 18, 70, 70, 70, 70, 51, 12, 1, 1, 1, 18, 9, 18, 70, 70] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) 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: REAL300000003250 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 33, 33, 79, 79, 79, 42, 79, 79, 79, 143, 201, 201, 201, 155, 201, 201, 201, 1, 1, 1, 1, 10, 33, 79, 39, 79, 201, 159, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003250 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003250 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003250/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003250 Building REAL300000003251 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003251' /scratch/stefan/7769584/working/building/REAL300000003251 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003251 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003251/0 /scratch/stefan/7769584/working/building/REAL300000003251 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/283 `/scratch/stefan/7769584/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003251 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=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.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 201, 201, 201, 128, 69, 69, 69, 35, 69, 69, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 69, 27, 6, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 555 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003251 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=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.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 23, 23, 23, 17, 23, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 41, 69, 69, 41, 41, 69, 69, 69, 69, 34, 34, 34, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 12, 41, 69, 69, 69, 69] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46]) 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: REAL300000003251 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=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.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 23, 61, 61, 168, 201, 201, 168, 168, 201, 201, 201, 201, 4, 4, 4, 1, 2, 2, 2, 1, 1, 23, 23, 23, 23, 61, 168, 201, 201, 201, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 36, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003251 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003251 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003251/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003251 Building REAL300000003252 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003252' /scratch/stefan/7769584/working/building/REAL300000003252 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003252 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003252/0 /scratch/stefan/7769584/working/building/REAL300000003252 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/284 `/scratch/stefan/7769584/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)C=C1) `REAL300000003252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003252 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 201, 178, 201, 201, 178, 59, 59, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 178, 59, 16, 16, 16, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39]) total number of confs: 615 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003252 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [95, 69, 95, 67, 95, 95, 67, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 9, 16, 16, 16, 95, 95, 95, 95, 67, 13, 1, 1, 1, 16, 16, 16, 16, 95, 95] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003252 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 40, 40, 104, 104, 104, 104, 104, 104, 104, 190, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 40, 104, 104, 104, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003252 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003252 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003252/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003252 Building REAL300000003253 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003253' /scratch/stefan/7769584/working/building/REAL300000003253 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003253 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003253/0 /scratch/stefan/7769584/working/building/REAL300000003253 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/285 `/scratch/stefan/7769584/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003253 none COC(=O)C1=CN=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 201, 142, 142, 142, 142, 33, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 142, 201, 201, 201, 142, 142, 33, 33, 33, 7, 1, 1, 1, 1, 142] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 407 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: REAL300000003253 none COC(=O)C1=CN=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 13, 76, 142, 142, 83, 103, 142, 142, 142, 142, 1, 13, 13, 13, 1, 1, 13, 13, 13, 76, 142, 142, 142, 142, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 22, 36, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 621 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003253 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003253 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003253/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003253 Building REAL300000003254 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003254' /scratch/stefan/7769584/working/building/REAL300000003254 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003254 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003254/0 /scratch/stefan/7769584/working/building/REAL300000003254 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/286 `/scratch/stefan/7769584/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003254 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 105, 157, 157, 105, 49, 49, 49, 49, 49, 49, 49, 25, 25, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 157, 157, 201, 201, 201, 157, 157, 49, 49, 49, 25, 6, 1, 1, 1, 1, 157, 157] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 559 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003254 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 8, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 49, 49, 27, 49, 49, 49, 49, 49, 29, 29, 65, 65, 65, 29, 29, 1, 1, 1, 7, 27, 49, 49, 49, 49, 29, 29] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003254 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 29, 29, 29, 29, 29, 29, 58, 58, 139, 157, 157, 151, 157, 157, 157, 157, 157, 1, 1, 7, 7, 7, 1, 1, 29, 29, 29, 58, 139, 157, 157, 157, 157, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 42, 43, 26, 27, 31] set([0, 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: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003254 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003254 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003254/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003254 Building REAL300000003255 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003255' /scratch/stefan/7769584/working/building/REAL300000003255 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003255 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003255/0 /scratch/stefan/7769584/working/building/REAL300000003255 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/287 `/scratch/stefan/7769584/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC(Br)=C2)C=C1) `REAL300000003255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003255 none O=C([O-])C1=CC=C(NN=CC2=CNC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 22, 34, 22, 34, 34, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 22, 7, 1, 1, 1, 34, 34] 34 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 25, 26]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003255 none O=C([O-])C1=CC=C(NN=CC2=CNC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 20, 21, 34, 34, 34, 34, 34, 1, 1, 1, 1, 11, 20, 34, 34, 34, 1, 1] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003255 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003255 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003255/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003255 Building REAL300000003256 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003256' /scratch/stefan/7769584/working/building/REAL300000003256 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003256 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003256/0 /scratch/stefan/7769584/working/building/REAL300000003256 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/288 `/scratch/stefan/7769584/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(F)=C1OC) `REAL300000003256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003256 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 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, 66, 66, 66, 65, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 82, 82, 82, 82, 66, 65, 33, 6, 1, 1, 1, 1, 82, 82, 82] 82 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) 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: REAL300000003256 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 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, 8, 8, 43, 65, 65, 43, 49, 65, 65, 65, 65, 1, 1, 1, 1, 6, 3, 3, 3, 1, 1, 8, 43, 64, 65, 65, 65, 7, 7, 7] 82 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29, 30, 31, 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/7769584/working/building/REAL300000003256 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003256 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003256/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003256 Building REAL300000003257 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003257' /scratch/stefan/7769584/working/building/REAL300000003257 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003257 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003257/0 /scratch/stefan/7769584/working/building/REAL300000003257 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/289 `/scratch/stefan/7769584/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003257 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=C(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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 81, 123, 123, 81, 123, 123, 123, 81, 81, 31, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 123, 123, 81, 123, 123, 123, 123, 82, 82, 82, 30, 6, 1, 1, 1, 1] 123 rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003257 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=C(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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 33, 33, 101, 123, 123, 123, 123, 123, 123, 123, 123, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 33, 101, 123, 123, 123, 123] 123 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, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003257 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=C(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', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 12, 12, 64, 81, 82, 80, 82, 82, 82, 82, 82, 2, 2, 2, 5, 5, 1, 5, 5, 5, 5, 2, 2, 2, 12, 63, 81, 82, 82, 82] 123 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003257 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003257 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003257/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003257 Building REAL300000003258 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003258' /scratch/stefan/7769584/working/building/REAL300000003258 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003258 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003258/0 /scratch/stefan/7769584/working/building/REAL300000003258 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/290 `/scratch/stefan/7769584/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1SC(F)(F)F) `REAL300000003258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003258 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1SC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 10 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003258 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1SC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 7 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003258 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003258 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003258/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003258 Building REAL300000003259 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003259' /scratch/stefan/7769584/working/building/REAL300000003259 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003259 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003259/0 /scratch/stefan/7769584/working/building/REAL300000003259 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/291 `/scratch/stefan/7769584/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC2=CC=CC=C12) `REAL300000003259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003259 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 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: [9, 1, 9, 9, 31, 57, 57, 31, 31, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 57, 57, 57, 57, 1, 1, 1, 1, 1] 57 rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003259 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 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: [31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 57, 57, 57, 57, 57, 57, 57, 57, 32, 32, 32, 6, 1, 1, 1, 1, 57, 57, 57, 57, 57] 57 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003259 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003259 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003259/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003259 Building REAL300000003260 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003260' /scratch/stefan/7769584/working/building/REAL300000003260 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003260 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003260/0 /scratch/stefan/7769584/working/building/REAL300000003260 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/292 `/scratch/stefan/7769584/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1) `REAL300000003260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003260 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 14, 8, 14, 14, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 14, 8, 2, 1, 1, 1, 1, 1, 14, 14] 14 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 18, 19, 22, 23, 24, 25, 26, 27]) 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: REAL300000003260 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 4, 14, 14, 14, 14, 14, 14, 1, 1] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003260 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003260/1 /scratch/stefan/7769584/working/building/REAL300000003260 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/293 `/scratch/stefan/7769584/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1) `REAL300000003260.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003260 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 28, 28] 28 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 18, 19, 22, 23, 24, 25, 26, 27]) 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: REAL300000003260 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 13, 13, 28, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003260 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003260 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003260/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003260/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003260 Building REAL300000003261 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003261' /scratch/stefan/7769584/working/building/REAL300000003261 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003261 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003261/0 /scratch/stefan/7769584/working/building/REAL300000003261 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/294 `/scratch/stefan/7769584/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000003261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003261 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [113, 69, 69, 69, 24, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 68, 69, 125, 147, 147, 155, 155, 113, 113, 113, 69, 23, 5, 1, 1, 1, 1, 69, 147, 147, 147, 147] 155 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003261 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 43, 69, 69, 43, 43, 69, 69, 69, 69, 1, 1, 1, 1, 1, 5, 14, 14, 21, 21, 4, 4, 4, 1, 8, 43, 69, 69, 69, 69, 1, 14, 14, 14, 14] 155 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003261 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003261 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003261/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003261 Building REAL300000003262 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003262' /scratch/stefan/7769584/working/building/REAL300000003262 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003262 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003262/0 /scratch/stefan/7769584/working/building/REAL300000003262 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/295 `/scratch/stefan/7769584/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1) `REAL300000003262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003262 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 1 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [44, 33, 44, 27, 44, 44, 27, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 44, 44, 44, 44, 27, 10, 1, 1, 2, 1, 44, 44] 88 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 26, 27, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 28, 30, 31]) 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: REAL300000003262 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 1 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, 6, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 6, 23, 44, 44, 88, 44, 1, 1] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003262 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003262 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003262/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003262 Building REAL300000003263 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003263' /scratch/stefan/7769584/working/building/REAL300000003263 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003263 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003263/0 /scratch/stefan/7769584/working/building/REAL300000003263 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/296 `/scratch/stefan/7769584/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300000003263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003263 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 84, 147, 84, 84, 84, 36, 36, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 84, 84, 84, 147, 147, 147, 84, 84, 36, 7, 1, 1, 1, 1, 84, 84, 84, 84] 147 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) 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: REAL300000003263 none COC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 11, 11, 58, 84, 84, 75, 84, 84, 84, 84, 84, 1, 1, 1, 13, 13, 13, 1, 1, 11, 58, 84, 84, 84, 84, 1, 2, 2, 2] 147 rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003263 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003263 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003263/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003263 Building REAL300000003264 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003264' /scratch/stefan/7769584/working/building/REAL300000003264 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003264 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003264/0 /scratch/stefan/7769584/working/building/REAL300000003264 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/297 `/scratch/stefan/7769584/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003264 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 25, 6, 1, 1, 1, 1, 46] 46 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003264 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 8, 8, 33, 46, 46, 33, 33, 46, 46, 46, 46, 1, 8, 33, 46, 46, 46, 46, 1] 46 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003264 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003264 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003264/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003264 Building REAL300000003265 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003265' /scratch/stefan/7769584/working/building/REAL300000003265 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003265 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003265/0 /scratch/stefan/7769584/working/building/REAL300000003265 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/298 `/scratch/stefan/7769584/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(F)(F)F)=C1) `REAL300000003265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003265 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 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, 2, 2, 7, 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: [12, 1, 12, 12, 50, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 50, 63, 63, 63, 63, 1, 1] 63 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 161 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003265 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 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, 2, 2, 7, 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: [29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 63, 63, 63, 63, 63, 63, 63, 63, 29, 29, 29, 7, 1, 1, 1, 1, 63, 63] 63 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003265 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003265 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003265/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003265 Building REAL300000003266 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003266' /scratch/stefan/7769584/working/building/REAL300000003266 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003266 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003266/0 /scratch/stefan/7769584/working/building/REAL300000003266 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/299 `/scratch/stefan/7769584/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC=CC=C1CC(C)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003266 none CCSC1=CC=CC=C1CC(C)N=NC1=CC=C(C(=O)[O-])C=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.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [201, 190, 124, 124, 124, 106, 124, 124, 72, 31, 5, 31, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 124, 124, 124, 124, 72, 72, 31, 31, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 649 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: REAL300000003266 none CCSC1=CC=CC=C1CC(C)N=NC1=CC=C(C(=O)[O-])C=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.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 82, 82, 124, 124, 82, 82, 124, 124, 124, 124, 30, 30, 30, 29, 29, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 124, 124, 124, 124] 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, 39, 40, 41]) total number of confs: 560 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003266 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003266 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003266/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003266 Building REAL300000003267 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003267' /scratch/stefan/7769584/working/building/REAL300000003267 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003267 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003267/0 /scratch/stefan/7769584/working/building/REAL300000003267 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/300 `/scratch/stefan/7769584/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CN2C(C)(C1)C(N=NC1=CC=C(C(=O)[O-])C=C1)CS2(=O)=O) `REAL300000003267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat geometry on atom 4 of molecule 'REAL300000003267' Warning: REAL300000003267 failed due to unspecified stereochemistry with strict stereo enabled Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat geometry on atom 4 of molecule 'REAL300000003267' Warning: REAL300000003267 failed due to unspecified stereochemistry with strict stereo enabled ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] Conformer generation failed Skipping REAL300000003267 0 /scratch/stefan/7769584/working/building/REAL300000003267 /scratch/stefan/7769584/working /scratch/stefan/7769584 `0' -> `0.failed' Finished preparing REAL300000003267 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Found failed protomers Marking REAL300000003267 as failed `/scratch/stefan/7769584/working/building/REAL300000003267' -> `/scratch/stefan/7769584/failed/REAL300000003267' Building REAL300000003268 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003268' /scratch/stefan/7769584/working/building/REAL300000003268 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003268 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003268/0 /scratch/stefan/7769584/working/building/REAL300000003268 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/301 `/scratch/stefan/7769584/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000003268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003268 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 27, 35, 35, 27, 27, 35, 35, 35, 35, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 27, 35, 35, 35, 35, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003268 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 35, 35, 22, 22, 35, 35, 35, 35, 35, 22, 22, 22, 5, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003268 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003268 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003268/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003268 Building REAL300000003269 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003269' /scratch/stefan/7769584/working/building/REAL300000003269 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003269 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003269/0 /scratch/stefan/7769584/working/building/REAL300000003269 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/302 `/scratch/stefan/7769584/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(F)C=C3F)C2)C=C1) `REAL300000003269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003269 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(F)C=C3F)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 31, 31, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 8, 8, 8, 8, 1, 1, 1, 8, 8, 31, 31] 31 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 54 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003269 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(F)C=C3F)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 15, 16, 15, 17, 17, 13, 13, 1, 1, 1, 1, 1, 8, 8, 4, 8, 8, 8, 8, 1, 17, 17, 17, 17, 1, 1, 1, 1, 8, 8, 8, 1, 1, 17, 17] 31 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 20, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31, 34, 35]) total number of confs: 61 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: REAL300000003269 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(F)C=C3F)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 21, 21, 21, 31, 31, 31, 31, 31, 31, 31, 21, 1, 1, 1, 1, 21, 21, 21, 21, 31, 31, 31, 21, 21, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003269 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003269 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003269/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003269 Building REAL300000003270 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003270' /scratch/stefan/7769584/working/building/REAL300000003270 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003270 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003270/0 /scratch/stefan/7769584/working/building/REAL300000003270 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/303 `/scratch/stefan/7769584/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1COC2=CC=CC=C2C1) `REAL300000003270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003270 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 46 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: REAL300000003270 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 17, 17, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003270 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003270 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003270/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003270 Building REAL300000003271 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003271' /scratch/stefan/7769584/working/building/REAL300000003271 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003271 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003271/0 /scratch/stefan/7769584/working/building/REAL300000003271 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/304 `/scratch/stefan/7769584/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)SC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003271 none CC1=C(Br)SC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 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] 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, 16, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 49, 49, 49, 16, 16, 1, 1, 1, 1] 49 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23]) 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: REAL300000003271 none CC1=C(Br)SC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 2, 2, 2, 9, 9, 49, 49, 49, 49] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003271 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003271 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003271/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003271 Building REAL300000003272 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003272' /scratch/stefan/7769584/working/building/REAL300000003272 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003272 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003272/0 /scratch/stefan/7769584/working/building/REAL300000003272 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/305 `/scratch/stefan/7769584/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(O)C=C1Cl) `REAL300000003272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003272 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [8, 1, 8, 8, 25, 35, 35, 25, 25, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 35, 35, 35, 35, 1, 1, 2, 1] 70 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 147 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: REAL300000003272 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 35, 35, 24, 34, 35, 35, 35, 24, 24, 24, 5, 1, 1, 1, 1, 35, 35, 70, 35] 70 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003272 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003272 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003272/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003272 Building REAL300000003273 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003273' /scratch/stefan/7769584/working/building/REAL300000003273 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003273 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003273/0 /scratch/stefan/7769584/working/building/REAL300000003273 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/306 `/scratch/stefan/7769584/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1) `REAL300000003273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003273 none CN1C=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 55, 55, 55, 31, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 74, 74, 74, 74, 74, 74, 30, 6, 1, 1, 1, 1, 55] 74 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 115 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003273 none CN1C=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 1, 1, 1, 1, 1, 7, 7, 35, 55, 55, 35, 43, 55, 55, 55, 55, 1, 1, 10, 11, 11, 11, 10, 10, 7, 35, 55, 55, 55, 55, 1] 74 rigid atoms, others: [34, 4, 5, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000003273 none CN1C=CC(C2=NC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 25, 64, 74, 74, 64, 74, 74, 74, 74, 74, 10, 10, 1, 2, 2, 2, 1, 1, 25, 64, 74, 74, 74, 74, 10] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003273 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003273 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003273/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003273 Building REAL300000003274 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003274' /scratch/stefan/7769584/working/building/REAL300000003274 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003274 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003274/0 /scratch/stefan/7769584/working/building/REAL300000003274 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/307 `/scratch/stefan/7769584/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=N1) `REAL300000003274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003274 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 8, 42, 42, 137, 145, 145, 137, 137, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 42, 137, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 1, 1, 1] 145 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 406 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003274 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [104, 104, 104, 39, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 103, 145, 145, 145, 145, 104, 104, 104, 104, 104, 38, 6, 1, 1, 1, 1, 145, 145, 145, 145, 145, 145, 145, 145, 145] 145 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 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: 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: REAL300000003274 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 77, 104, 104, 77, 77, 104, 104, 104, 104, 1, 1, 8, 8, 8, 8, 1, 2, 2, 2, 1, 12, 76, 104, 104, 104, 103, 8, 8, 8, 8, 8, 8, 8, 8, 8] 145 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 395 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003274 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003274 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003274/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003274 Building REAL300000003275 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003275' /scratch/stefan/7769584/working/building/REAL300000003275 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003275 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003275/0 /scratch/stefan/7769584/working/building/REAL300000003275 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/308 `/scratch/stefan/7769584/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21) `REAL300000003275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003275 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 38, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 38, 38, 38, 6, 1, 1, 1, 1, 112, 112, 112, 112, 112] 112 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 164 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: REAL300000003275 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 12, 12, 12, 68, 112, 112, 81, 100, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 13, 13, 13, 68, 112, 112, 112, 112, 1, 1, 1, 1, 1] 112 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 407 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003275 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003275 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003275/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003275 Building REAL300000003276 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003276' /scratch/stefan/7769584/working/building/REAL300000003276 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003276 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003276/0 /scratch/stefan/7769584/working/building/REAL300000003276 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/309 `/scratch/stefan/7769584/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003276 none CC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 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, 22, 30, 30, 22, 22, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 22, 7, 1, 1, 1, 1] 30 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003276 none CC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 30, 30, 27, 30, 30, 30, 30, 30, 1, 1, 2, 2, 2, 1, 1, 1, 8, 24, 30, 30, 30, 30] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 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/7769584/working/building/REAL300000003276 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003276 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003276/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003276 Building REAL300000003277 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003277' /scratch/stefan/7769584/working/building/REAL300000003277 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003277 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003277/0 /scratch/stefan/7769584/working/building/REAL300000003277 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/310 `/scratch/stefan/7769584/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1) `REAL300000003277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003277 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 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, 201, 190, 73, 73, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 190, 73, 19, 19, 19, 1, 1, 1, 1, 19, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003277 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 55, 56, 36, 56, 56, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 56, 56, 56, 56, 36, 7, 1, 1, 1, 19, 19, 19, 19, 1, 56, 56] 201 rigid atoms, others: [32, 37, 9, 10, 11, 12, 13, 14, 15, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38, 39]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003277 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 21, 21, 56, 56, 56, 56, 56, 171, 201, 201, 201, 201, 201, 201, 56, 1, 1, 1, 1, 8, 21, 56, 56, 56, 201, 201, 201, 201, 56, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003277 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003277 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003277/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003277 Building REAL300000003278 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003278' /scratch/stefan/7769584/working/building/REAL300000003278 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003278 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003278/0 /scratch/stefan/7769584/working/building/REAL300000003278 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/311 `/scratch/stefan/7769584/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003278 none CN(C)C(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 51, 18, 18, 18, 18, 12, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 51, 51, 51, 51, 51, 51, 18, 18, 18, 11, 5, 1, 1, 1, 1, 18] 51 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003278 none CN(C)C(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 18, 10, 12, 18, 18, 18, 18, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 4, 10, 18, 18, 18, 18, 1] 51 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22, 38, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003278 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003278 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003278/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003278 Building REAL300000003279 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003279' /scratch/stefan/7769584/working/building/REAL300000003279 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003279 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003279/0 /scratch/stefan/7769584/working/building/REAL300000003279 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/312 `/scratch/stefan/7769584/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1) `REAL300000003279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003279 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 19, 72, 72, 173, 201, 201, 174, 201, 201, 201, 201, 201, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 72, 72, 72, 173, 201, 201, 201, 201, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 656 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003279 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 107, 107, 54, 71, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 10, 10, 10, 53, 107, 107, 107, 107, 1, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 534 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003279 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 107, 107, 107, 107, 107, 167, 201, 201, 201, 31, 31, 31, 5, 1, 1, 1, 1, 107, 107, 167, 167, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 607 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003279 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003279 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003279/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003279 Building REAL300000003280 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003280' /scratch/stefan/7769584/working/building/REAL300000003280 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003280 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003280/0 /scratch/stefan/7769584/working/building/REAL300000003280 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/313 `/scratch/stefan/7769584/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1) `REAL300000003280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003280 none O=C([O-])C1=CC=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 63, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 63, 63, 12, 12, 1, 1, 2, 1, 201, 201] 402 rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003280 none O=C([O-])C1=CC=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [82, 65, 82, 65, 82, 82, 64, 64, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 82, 82, 82, 82, 9, 9, 1, 1, 12, 12, 24, 12, 82, 82] 402 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003280 none O=C([O-])C1=CC=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 92, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 1, 1, 1, 1, 27, 27, 92, 92, 201, 201, 402, 201, 1, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] 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]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003280 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003280/1 /scratch/stefan/7769584/working/building/REAL300000003280 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/314 `/scratch/stefan/7769584/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1) `REAL300000003280.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003280 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 36, 36, 36, 36, 36, 36, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 36, 36, 36, 36, 36, 10, 10, 10, 1, 1, 2, 1, 36, 36] 72 rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003280 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 10, 12, 10, 12, 12, 10, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 12, 12, 12, 12, 10, 2, 1, 1, 10, 10, 20, 10, 12, 12] 72 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) 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: REAL300000003280 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 232 conformations in input total number of sets (complete confs): 232 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 36, 36, 65, 65, 65, 65, 116, 116, 116, 116, 116, 116, 116, 116, 116, 65, 1, 1, 1, 1, 9, 36, 65, 65, 116, 116, 232, 116, 1, 1] 232 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003280 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003280 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003280/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003280/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003280 Building REAL300000003281 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003281' /scratch/stefan/7769584/working/building/REAL300000003281 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003281 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003281/0 /scratch/stefan/7769584/working/building/REAL300000003281 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/315 `/scratch/stefan/7769584/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1S(N)(=O)=O) `REAL300000003281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003281 none CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1S(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 6, 6, 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: [93, 93, 93, 93, 40, 40, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 112, 112, 112, 93, 93, 93, 93, 40, 7, 1, 1, 1, 1, 112, 112] 112 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003281 none CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1S(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 6, 6, 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, 10, 10, 68, 93, 93, 68, 76, 93, 93, 93, 93, 1, 1, 5, 5, 5, 2, 2, 2, 1, 10, 68, 93, 93, 93, 93, 5, 5] 112 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003281 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003281 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003281/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003281 Building REAL300000003282 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003282' /scratch/stefan/7769584/working/building/REAL300000003282 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003282 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003282/0 /scratch/stefan/7769584/working/building/REAL300000003282 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/316 `/scratch/stefan/7769584/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(C3CC3)NN=C2Cl)C=C1) `REAL300000003282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003282 none O=C([O-])C1=CC=C(NN=CC2=C(C3CC3)NN=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 110, 116, 116, 110, 48, 48, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 116, 116, 116, 116, 110, 48, 1, 1, 1, 1, 1, 7, 116, 116] 116 rigid atoms, others: [11, 12, 13, 14, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32]) total number of confs: 316 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003282 none O=C([O-])C1=CC=C(NN=CC2=C(C3CC3)NN=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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: [100, 81, 100, 73, 100, 100, 73, 12, 12, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1, 100, 100, 100, 100, 73, 12, 7, 7, 7, 7, 7, 1, 100, 100] 116 rigid atoms, others: [9, 10, 11, 12, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) 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: REAL300000003282 none O=C([O-])C1=CC=C(NN=CC2=C(C3CC3)NN=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 39, 39, 93, 93, 113, 113, 93, 93, 93, 93, 1, 1, 1, 1, 11, 39, 113, 113, 113, 113, 113, 93, 1, 1] 113 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003282 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003282 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003282/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003282 Building REAL300000003283 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003283' /scratch/stefan/7769584/working/building/REAL300000003283 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003283 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003283/0 /scratch/stefan/7769584/working/building/REAL300000003283 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/317 `/scratch/stefan/7769584/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)C=C1) `REAL300000003283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003283 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 95, 84, 95, 95, 84, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 95, 95, 95, 95, 84, 26, 1, 1, 1, 1, 6, 6, 6, 95, 95] 95 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 289 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003283 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [93, 64, 93, 64, 93, 93, 64, 12, 12, 1, 1, 1, 1, 6, 6, 2, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 64, 12, 6, 6, 6, 6, 1, 1, 1, 93, 93] 95 rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003283 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 42, 42, 93, 93, 95, 95, 95, 95, 95, 95, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 12, 42, 95, 95, 95, 95, 93, 93, 93, 1, 1] 95 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003283 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003283 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003283/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003283 Building REAL300000003284 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003284' /scratch/stefan/7769584/working/building/REAL300000003284 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003284 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003284/0 /scratch/stefan/7769584/working/building/REAL300000003284 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/318 `/scratch/stefan/7769584/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1) `REAL300000003284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003284 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 122, 122, 191, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 6, 1, 1, 1, 1, 1, 31, 31, 122, 122, 122, 191, 201, 201, 201, 201, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 31] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41]) total number of confs: 526 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003284 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 105, 106, 62, 106, 106, 106, 106, 106, 1, 1, 1, 1, 9, 31, 31, 31, 1, 1, 13, 13, 13, 56, 105, 105, 106, 106, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31, 1] 201 rigid atoms, others: [1, 41, 13, 14, 15, 16, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 503 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003284 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 106, 106, 106, 183, 201, 201, 201, 106, 105, 23, 23, 23, 5, 1, 1, 1, 1, 106, 183, 183, 201, 201, 201, 201, 201, 201, 201, 105] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 602 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003284 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003284 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003284/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003284 Building REAL300000003285 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003285' /scratch/stefan/7769584/working/building/REAL300000003285 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003285 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003285/0 /scratch/stefan/7769584/working/building/REAL300000003285 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/319 `/scratch/stefan/7769584/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=NC(C(F)(F)F)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003285 none CN(C)C1=NC(C(F)(F)F)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 37, 31, 31, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 31, 7, 1, 1, 1, 1] 37 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003285 none CN(C)C1=NC(C(F)(F)F)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 27, 37, 37, 27, 27, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 1, 1, 7, 27, 37, 37, 37, 37] 37 rigid atoms, others: [32, 1, 3, 4, 5, 6, 10, 11, 12, 13, 31] set([0, 2, 7, 8, 9, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003285 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003285 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003285/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003285 Building REAL300000003286 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003286' /scratch/stefan/7769584/working/building/REAL300000003286 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003286 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003286/0 /scratch/stefan/7769584/working/building/REAL300000003286 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/320 `/scratch/stefan/7769584/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=CC([N+](=O)[O-])=C1) `REAL300000003286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003286 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=CC([N+](=O)[O-])=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 34, 33, 33, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 34, 34, 34, 5, 1, 1, 1, 1, 126, 127] 127 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 177 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: REAL300000003286 none COC1=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=CC([N+](=O)[O-])=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 1, 1, 1, 1, 12, 12, 12, 73, 126, 126, 73, 113, 126, 126, 126, 126, 1, 1, 1, 2, 2, 1, 3, 3, 3, 1, 13, 13, 13, 73, 126, 126, 127, 127, 1, 1] 127 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 23, 36, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 530 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003286 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003286 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003286/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003286 Building REAL300000003287 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003287' /scratch/stefan/7769584/working/building/REAL300000003287 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003287 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003287/0 /scratch/stefan/7769584/working/building/REAL300000003287 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/321 `/scratch/stefan/7769584/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1) `REAL300000003287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003287 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(S(=O)(=O)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 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, 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, 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: [12, 1, 12, 12, 53, 107, 107, 53, 95, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 1, 12, 12, 12, 53, 107, 107, 107, 107, 1, 1, 1, 1] 153 rigid atoms, others: [1, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 472 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: REAL300000003287 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(S(=O)(=O)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 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, 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, 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: [38, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 107, 107, 79, 107, 107, 153, 153, 153, 153, 153, 153, 107, 39, 39, 39, 6, 1, 1, 1, 1, 107, 107, 106, 107] 153 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 557 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003287 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003287 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003287/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003287 Building REAL300000003288 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003288' /scratch/stefan/7769584/working/building/REAL300000003288 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003288 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003288/0 /scratch/stefan/7769584/working/building/REAL300000003288 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/322 `/scratch/stefan/7769584/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1) `REAL300000003288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003288 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 68, 73, 68, 73, 73, 68, 29, 29, 7, 6, 6, 7, 1, 1, 1, 1, 1, 1, 1, 7, 73, 73, 73, 73, 68, 29, 7, 7, 1, 1, 1, 1, 1, 7, 73, 73] 73 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, 36]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003288 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [53, 39, 53, 39, 53, 53, 39, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 53, 53, 53, 53, 39, 8, 1, 1, 7, 7, 1, 7, 7, 1, 54, 54] 73 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 35, 36]) 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: REAL300000003288 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=C3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 36, 37, 54, 54, 54, 54, 73, 73, 54, 73, 73, 54, 1, 1, 1, 1, 10, 36, 54, 54, 73, 73, 54, 73, 73, 54, 1, 1] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003288 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003288 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003288/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003288 Building REAL300000003289 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003289' /scratch/stefan/7769584/working/building/REAL300000003289 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003289 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003289/0 /scratch/stefan/7769584/working/building/REAL300000003289 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/323 `/scratch/stefan/7769584/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1) `REAL300000003289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003289 none O=C([O-])C1=CC=C(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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, 61, 87, 61, 87, 87, 61, 24, 24, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 87, 87, 87, 87, 61, 24, 12, 13, 1, 1, 1, 1, 87, 87] 87 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 319 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003289 none O=C([O-])C1=CC=C(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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: [48, 30, 48, 30, 48, 48, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 48, 48, 48, 48, 30, 7, 1, 1, 13, 13, 12, 13, 48, 48] 87 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003289 none O=C([O-])C1=CC=C(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 46, 46, 46, 46, 46, 77, 77, 77, 77, 77, 46, 1, 1, 1, 1, 7, 31, 46, 46, 77, 77, 77, 77, 1, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003289 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003289/1 /scratch/stefan/7769584/working/building/REAL300000003289 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/324 `/scratch/stefan/7769584/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CC=NC(C3=CC=CC=N3)=N2)C=C1) `REAL300000003289.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003289 none O=C([O-])C1=CC=C(N=NCC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 201, 196, 201, 201, 195, 195, 58, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 58, 58, 12, 13, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003289 none O=C([O-])C1=CC=C(N=NCC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [101, 72, 101, 72, 101, 101, 71, 71, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 101, 101, 101, 101, 9, 9, 1, 1, 13, 13, 12, 13, 101, 101] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003289 none O=C([O-])C1=CC=C(N=NCC2=CC=NC(C3=CC=CC=N3)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 37, 120, 120, 120, 114, 120, 201, 201, 201, 201, 201, 120, 1, 1, 1, 1, 37, 37, 120, 120, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003289 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003289 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003289/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003289/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003289 Building REAL300000003290 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003290' /scratch/stefan/7769584/working/building/REAL300000003290 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003290 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003290/0 /scratch/stefan/7769584/working/building/REAL300000003290 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/325 `/scratch/stefan/7769584/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C(Br)N1) `REAL300000003290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003290 none CC1=NC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C(Br)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 19, 19, 1, 1, 1, 1, 40] 40 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003290 none CC1=NC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C(Br)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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, 8, 38, 38, 40, 40, 38, 38, 40, 40, 40, 40, 1, 1, 1, 2, 2, 2, 8, 8, 40, 40, 40, 40, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003290 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003290 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003290/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003290 Building REAL300000003291 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003291' /scratch/stefan/7769584/working/building/REAL300000003291 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003291 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003291/0 /scratch/stefan/7769584/working/building/REAL300000003291 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/326 `/scratch/stefan/7769584/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCC3(CS(=O)(=O)C3)CC2)C=C1) `REAL300000003291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003291 none O=C([O-])C1=CC=C(N=NC2CCC3(CS(=O)(=O)C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 38, 37]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003291 none O=C([O-])C1=CC=C(N=NC2CCC3(CS(=O)(=O)C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003291 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003291 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003291/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003291 Building REAL300000003292 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003292' /scratch/stefan/7769584/working/building/REAL300000003292 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003292 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003292/0 /scratch/stefan/7769584/working/building/REAL300000003292 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/327 `/scratch/stefan/7769584/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003292 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 32, 32, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 61, 32, 7, 1, 1, 1, 1] 61 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 95 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: REAL300000003292 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 47, 61, 61, 48, 61, 61, 61, 61, 61, 4, 4, 4, 4, 4, 4, 1, 1, 1, 12, 47, 61, 61, 61, 61] 61 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 30, 31] set([0, 2, 8, 9, 13, 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: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003292 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003292 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003292/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003292 Building REAL300000003293 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003293' /scratch/stefan/7769584/working/building/REAL300000003293 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003293 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003293/0 /scratch/stefan/7769584/working/building/REAL300000003293 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/328 `/scratch/stefan/7769584/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=C1Cl) `REAL300000003293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003293 none CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 16, 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, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 11, 10, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 10] 11 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003293 none CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)C(=O)NC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 16, 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, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 10, 10, 7, 7, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 10, 10, 10, 10, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 17, 18, 19, 20, 21, 22, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003293 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003293 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003293/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003293 Building REAL300000003294 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003294' /scratch/stefan/7769584/working/building/REAL300000003294 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003294 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003294/0 /scratch/stefan/7769584/working/building/REAL300000003294 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/329 `/scratch/stefan/7769584/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C2CCCCC2=N1) `REAL300000003294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003294 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C2CCCCC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 7, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 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: REAL300000003294 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C2CCCCC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 38, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 38, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 37, 35, 33, 40, 39, 34, 16, 17, 18, 19, 20, 21, 22, 36, 26, 38] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003294 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003294 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003294/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003294 Building REAL300000003295 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003295' /scratch/stefan/7769584/working/building/REAL300000003295 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003295 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003295/0 /scratch/stefan/7769584/working/building/REAL300000003295 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/330 `/scratch/stefan/7769584/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2CCCCC2)C=C1) `REAL300000003295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003295 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 29, 10, 10, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 29, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 33 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43]) total number of confs: 83 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003295 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 33, 28, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33] 33 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003295 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 25 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003295 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003295 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003295/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003295 Building REAL300000003296 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003296' /scratch/stefan/7769584/working/building/REAL300000003296 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003296 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003296/0 /scratch/stefan/7769584/working/building/REAL300000003296 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/331 `/scratch/stefan/7769584/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CSC(C(F)(F)F)=N2)C=C1) `REAL300000003296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003296 none O=C([O-])C1=CC=C(NN=CC2=CSC(C(F)(F)F)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 27, 27, 22, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 26, 27, 27, 27, 21, 6, 1, 26, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 20, 21, 22, 23, 24, 26, 27]) 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: REAL300000003296 none O=C([O-])C1=CC=C(NN=CC2=CSC(C(F)(F)F)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 11, 26, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003296 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003296 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003296/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003296 Building REAL300000003297 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003297' /scratch/stefan/7769584/working/building/REAL300000003297 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003297 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003297/0 /scratch/stefan/7769584/working/building/REAL300000003297 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/332 `/scratch/stefan/7769584/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1) `REAL300000003297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003297 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 48, 62, 48, 62, 62, 48, 25, 25, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 62, 62, 62, 62, 48, 25, 6, 6, 1, 1, 1, 1, 62, 62] 62 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003297 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 50, 33, 50, 50, 33, 9, 9, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 5, 5, 6, 6, 1, 50, 50, 50, 50, 33, 9, 1, 1, 6, 6, 6, 6, 50, 50] 62 rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) 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: REAL300000003297 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 50, 50, 50, 50, 62, 62, 50, 50, 62, 62, 62, 62, 50, 1, 1, 1, 1, 8, 32, 50, 50, 62, 62, 62, 62, 1, 1] 62 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003297 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003297 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003297/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003297 Building REAL300000003298 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003298' /scratch/stefan/7769584/working/building/REAL300000003298 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003298 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003298/0 /scratch/stefan/7769584/working/building/REAL300000003298 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/333 `/scratch/stefan/7769584/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2Br)C=C1) `REAL300000003298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003298 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 28, 8, 1, 1, 1, 31, 31] 31 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003298 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 26, 26, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 8, 26, 31, 31, 31, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003298 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003298 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003298/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003298 Building REAL300000003299 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003299' /scratch/stefan/7769584/working/building/REAL300000003299 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003299 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003299/0 /scratch/stefan/7769584/working/building/REAL300000003299 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/334 `/scratch/stefan/7769584/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)F)C(F)=C2)C=C1) `REAL300000003299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003299 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)F)C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [92, 79, 92, 64, 92, 92, 60, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 92, 92, 92, 92, 60, 11, 1, 1, 11, 1, 92, 92] 105 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 26, 27, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 28, 30, 31]) 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: REAL300000003299 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)F)C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 40, 40, 91, 91, 91, 91, 103, 103, 91, 91, 91, 1, 1, 1, 1, 11, 40, 91, 91, 103, 91, 1, 1] 103 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003299 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003299 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003299/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003299 Building REAL300000003300 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003300' /scratch/stefan/7769584/working/building/REAL300000003300 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003300 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003300/0 /scratch/stefan/7769584/working/building/REAL300000003300 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/335 `/scratch/stefan/7769584/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Cl) `REAL300000003300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003300 none CC1=C(Cl)C=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', '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', '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, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 19, 19, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 25, 25, 25, 19, 7, 1, 1, 1, 1] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003300 none CC1=C(Cl)C=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', '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', '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, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2, 1, 1, 8, 21, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 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/7769584/working/building/REAL300000003300 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003300 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003300/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003300 Building REAL300000003301 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003301' /scratch/stefan/7769584/working/building/REAL300000003301 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003301 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003301/0 /scratch/stefan/7769584/working/building/REAL300000003301 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/336 `/scratch/stefan/7769584/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)C=C1I) `REAL300000003301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003301 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)C=C1I 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'I', '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, 1, 11, 11, 1, 1, 1, 5, 1, 1, 18, 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, 2, 2, 7, 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, 26, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 27, 37, 38, 38, 38, 38, 25, 6, 1, 1, 1, 1, 38, 38, 38, 38] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 34, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003301 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)C=C1I 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'I', '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, 1, 11, 11, 1, 1, 1, 5, 1, 1, 18, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 34, 38, 38, 34, 34, 38, 38, 38, 38, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 34, 38, 38, 38, 38, 2, 2, 2, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 34, 16, 17, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003301 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003301 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003301/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003301 Building REAL300000003302 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003302' /scratch/stefan/7769584/working/building/REAL300000003302 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003302 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003302/0 /scratch/stefan/7769584/working/building/REAL300000003302 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/337 `/scratch/stefan/7769584/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003302 none N#CC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 21, 6, 1, 1, 1, 1, 35] 35 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 29]) 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: REAL300000003302 none N#CC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 31, 35, 35, 31, 31, 35, 35, 35, 35, 1, 1, 1, 8, 31, 35, 35, 35, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003302 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003302 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003302/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003302 Building REAL300000003303 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003303' /scratch/stefan/7769584/working/building/REAL300000003303 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003303 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003303/0 /scratch/stefan/7769584/working/building/REAL300000003303 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/338 `/scratch/stefan/7769584/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003303 none CSCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 110, 41, 41, 97, 97, 41, 41, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 97, 97, 149, 151, 151, 110, 110, 97, 97, 41, 7, 1, 1, 1, 1, 97, 97] 151 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003303 none CSCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [20, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 97, 97, 72, 97, 97, 97, 97, 97, 1, 1, 20, 20, 20, 4, 4, 1, 1, 11, 56, 97, 97, 97, 97, 1, 1] 151 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 34, 19, 20, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003303 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003303 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003303/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003303 Building REAL300000003304 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003304' /scratch/stefan/7769584/working/building/REAL300000003304 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003304 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003304/0 /scratch/stefan/7769584/working/building/REAL300000003304 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/339 `/scratch/stefan/7769584/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCOCC2=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003304 none CN1N=C2CCOCC2=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 5, 1, 1, 1, 1] 40 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003304 none CN1N=C2CCOCC2=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 34, 40, 40, 37, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 34, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003304 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003304 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003304/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003304 Building REAL300000003305 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003305' /scratch/stefan/7769584/working/building/REAL300000003305 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003305 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003305/0 /scratch/stefan/7769584/working/building/REAL300000003305 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/340 `/scratch/stefan/7769584/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003305 none COC(=O)C(C)OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 146, 201, 108, 146, 51, 51, 51, 23, 51, 51, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 146, 146, 146, 146, 51, 51, 51, 51, 20, 4, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 668 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: REAL300000003305 none COC(=O)C(C)OC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 21, 46, 9, 21, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 51, 51, 29, 29, 51, 51, 51, 51, 46, 46, 46, 21, 21, 21, 21, 1, 1, 1, 1, 9, 29, 51, 51, 51, 51] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 363 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003305 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003305 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003305/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003305 Building REAL300000003306 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003306' /scratch/stefan/7769584/working/building/REAL300000003306 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003306 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003306/0 /scratch/stefan/7769584/working/building/REAL300000003306 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/341 `/scratch/stefan/7769584/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003306 none COC(=O)COC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 201, 77, 29, 29, 29, 16, 29, 29, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 166, 166, 29, 29, 29, 29, 16, 5, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 682 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003306 none COC(=O)COC1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 40, 130, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 29, 29, 20, 20, 29, 29, 29, 29, 130, 130, 130, 40, 40, 1, 1, 1, 1, 4, 20, 29, 29, 29, 29] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003306 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003306 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003306/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003306 Building REAL300000003307 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003307' /scratch/stefan/7769584/working/building/REAL300000003307 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003307 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003307/0 /scratch/stefan/7769584/working/building/REAL300000003307 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/342 `/scratch/stefan/7769584/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)C2)CC1) `REAL300000003307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003307 none CC(C)(C)OC(=O)N1CCC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 29, 16, 29, 16, 16, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 54, 54, 54, 54, 54, 54, 54, 54, 54, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16] 54 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003307 none CC(C)(C)OC(=O)N1CCC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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, 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: [21, 18, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 16, 16, 12, 13, 16, 16, 16, 16, 1, 1, 1, 22, 22, 22, 22, 21, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1] 54 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003307 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003307 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003307/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003307 Building REAL300000003308 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003308' /scratch/stefan/7769584/working/building/REAL300000003308 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003308 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003308/0 /scratch/stefan/7769584/working/building/REAL300000003308 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/343 `/scratch/stefan/7769584/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000003308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003308 none CC(C)(C)OC(=O)NCC1CCC(N=NC2=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 181, 143, 181, 66, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 66, 66, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 23, 23] 201 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003308 none CC(C)(C)OC(=O)NCC1CCC(N=NC2=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 76, 78, 78, 56, 33, 56, 7, 1, 1, 1, 1, 1, 1, 13, 13, 23, 23, 13, 13, 23, 23, 23, 23, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78, 33, 7, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003308 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003308 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003308/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003308 Building REAL300000003309 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003309' /scratch/stefan/7769584/working/building/REAL300000003309 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003309 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003309/0 /scratch/stefan/7769584/working/building/REAL300000003309 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/344 `/scratch/stefan/7769584/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1) `REAL300000003309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003309 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need 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, 183, 201, 201, 183, 69, 69, 31, 31, 31, 30, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 183, 69, 31, 30, 31, 31, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39]) total number of confs: 631 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003309 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 57, 31, 57, 57, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 31, 57, 57, 57, 57, 30, 8, 1, 1, 1, 1, 31, 31, 31, 31, 57, 57] 201 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]) 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: REAL300000003309 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 34, 34, 63, 63, 40, 63, 63, 63, 124, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 8, 34, 63, 64, 63, 63, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003309 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003309 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003309/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003309 Building REAL300000003310 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003310' /scratch/stefan/7769584/working/building/REAL300000003310 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003310 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003310/0 /scratch/stefan/7769584/working/building/REAL300000003310 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/345 `/scratch/stefan/7769584/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003310 none COC1=CC=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 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, 84, 84, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 40, 7, 1, 1, 1, 1] 84 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300000003310 none COC1=CC=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 84, 84, 67, 84, 84, 84, 84, 84, 1, 1, 4, 4, 4, 1, 1, 2, 2, 2, 7, 49, 84, 84, 84, 84] 84 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003310 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003310 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003310/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003310 Building REAL300000003311 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003311' /scratch/stefan/7769584/working/building/REAL300000003311 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003311 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003311/0 /scratch/stefan/7769584/working/building/REAL300000003311 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/346 `/scratch/stefan/7769584/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(C2=CC=CC=C2)CC(N=NC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000003311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003311 none COC(=O)C1(C2=CC=CC=C2)CC(N=NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [31, 31, 15, 31, 15, 15, 23, 23, 22, 23, 23, 15, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 31, 31, 31, 23, 23, 22, 23, 23, 15, 15, 15, 1, 1, 1, 1, 15, 15] 41 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 103 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003311 none COC(=O)C1(C2=CC=CC=C2)CC(N=NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 23, 23, 22, 23, 23, 23, 23, 23, 5, 17, 17, 17, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 5, 5] 41 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 28, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003311 none COC(=O)C1(C2=CC=CC=C2)CC(N=NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 11, 11, 15, 15, 12, 13, 15, 15, 15, 15, 1, 11, 11, 11, 5, 5, 3, 5, 5, 1, 1, 1, 15, 15, 15, 15, 1, 1] 41 rigid atoms, others: [33, 2, 35, 4, 5, 40, 41, 11, 12, 34, 13, 24] set([0, 1, 3, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003311 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003311 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003311/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003311 Building REAL300000003312 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003312' /scratch/stefan/7769584/working/building/REAL300000003312 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003312 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003312/0 /scratch/stefan/7769584/working/building/REAL300000003312 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/347 `/scratch/stefan/7769584/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCC3=C(C=CS3)C2)C=C1) `REAL300000003312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003312 none O=C([O-])C1=CC=C(N=NC2CCCC3=C(C=CS3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 22, 35]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003312 none O=C([O-])C1=CC=C(N=NC2CCCC3=C(C=CS3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 35] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003312 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003312 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003312/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003312 Building REAL300000003313 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003313' /scratch/stefan/7769584/working/building/REAL300000003313 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003313 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003313/0 /scratch/stefan/7769584/working/building/REAL300000003313 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/348 `/scratch/stefan/7769584/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1) `REAL300000003313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003313 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 65, 65, 177, 201, 201, 195, 201, 201, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 65, 65, 65, 177, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 524 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003313 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 85, 85, 43, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 36, 85, 85, 85, 85, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 35, 36, 41, 42, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 335 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003313 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 26, 85, 85, 52, 85, 192, 201, 201, 201, 201, 201, 201, 85, 85, 26, 26, 26, 6, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 85, 85] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 11, 12, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 449 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003313 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003313 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003313/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003313 Building REAL300000003314 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003314' /scratch/stefan/7769584/working/building/REAL300000003314 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003314 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003314/0 /scratch/stefan/7769584/working/building/REAL300000003314 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/349 `/scratch/stefan/7769584/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=CN=C2C=C1) `REAL300000003314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003314 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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] 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: [11, 1, 11, 11, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 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: REAL300000003314 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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] 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: [27, 27, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 7, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003314 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003314 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003314/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003314 Building REAL300000003315 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003315' /scratch/stefan/7769584/working/building/REAL300000003315 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003315 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003315/0 /scratch/stefan/7769584/working/building/REAL300000003315 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/350 `/scratch/stefan/7769584/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003315 none CN(C)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 32, 72, 32, 59, 59, 32, 32, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 59, 72, 72, 72, 72, 72, 72, 59, 59, 32, 7, 1, 1, 1, 1, 59, 59] 72 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 263 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003315 none CN(C)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 46, 59, 59, 54, 59, 59, 59, 59, 59, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 9, 46, 59, 59, 59, 59, 1, 1] 72 rigid atoms, others: [3, 5, 6, 7, 8, 9, 21, 22, 38, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003315 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003315 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003315/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003315 Building REAL300000003316 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003316' /scratch/stefan/7769584/working/building/REAL300000003316 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003316 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003316/0 /scratch/stefan/7769584/working/building/REAL300000003316 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/351 `/scratch/stefan/7769584/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003316 none CCN(CC)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [133, 85, 81, 85, 100, 39, 81, 39, 81, 81, 39, 39, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 81, 81, 133, 133, 133, 133, 133, 100, 100, 100, 100, 100, 81, 81, 39, 7, 1, 1, 1, 1, 81, 81] 160 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 742 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003316 none CCN(CC)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 6, 4, 6, 9, 1, 4, 1, 1, 1, 1, 1, 8, 8, 56, 81, 81, 61, 81, 81, 81, 81, 81, 1, 1, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 1, 1, 8, 56, 81, 81, 81, 81, 1, 1] 160 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 44, 43, 23, 24] 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, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003316 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003316 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003316/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003316 Building REAL300000003317 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003317' /scratch/stefan/7769584/working/building/REAL300000003317 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003317 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003317/0 /scratch/stefan/7769584/working/building/REAL300000003317 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/352 `/scratch/stefan/7769584/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003317 none CCNC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 104, 104, 42, 104, 42, 95, 95, 42, 42, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 95, 95, 114, 114, 114, 114, 114, 104, 95, 95, 42, 7, 1, 1, 1, 1, 95, 95] 114 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003317 none CCNC(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 8, 8, 63, 95, 95, 73, 95, 95, 95, 95, 95, 1, 1, 13, 13, 13, 13, 13, 4, 1, 1, 8, 63, 95, 95, 95, 95, 1, 1] 114 rigid atoms, others: [3, 5, 6, 7, 8, 9, 21, 22, 38, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003317 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003317 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003317/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003317 Building REAL300000003318 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003318' /scratch/stefan/7769584/working/building/REAL300000003318 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003318 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003318/0 /scratch/stefan/7769584/working/building/REAL300000003318 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/353 `/scratch/stefan/7769584/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2SC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC2=C1) `REAL300000003318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003318 none COC1=CC=C2SC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 14, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 59, 59, 59, 59, 59, 59, 36, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 59, 59, 61, 61, 61, 59, 59, 35, 6, 1, 1, 1, 1, 58, 58] 61 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003318 none COC1=CC=C2SC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 14, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 40, 58, 59, 44, 49, 59, 59, 59, 59, 1, 1, 1, 3, 3, 3, 1, 1, 6, 39, 58, 58, 59, 59, 1, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003318 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003318 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003318/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003318 Building REAL300000003319 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003319' /scratch/stefan/7769584/working/building/REAL300000003319 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003319 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003319/0 /scratch/stefan/7769584/working/building/REAL300000003319 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/354 `/scratch/stefan/7769584/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)C=C1) `REAL300000003319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003319 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 7, 1, 1, 1, 11, 11] 11 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003319 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 7, 10, 10, 10, 1, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003319 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003319 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003319/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003319 Building REAL300000003320 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003320' /scratch/stefan/7769584/working/building/REAL300000003320 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003320 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003320/0 /scratch/stefan/7769584/working/building/REAL300000003320 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/355 `/scratch/stefan/7769584/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=NO2)C=C1) `REAL300000003320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003320 none O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 123, 124, 124, 121, 121, 33, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 124, 124, 124, 124, 33, 33, 7, 1, 1, 1, 1, 1, 124, 124] 124 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: 229 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003320 none O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 84, 124, 124, 73, 73, 9, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 124, 124, 124, 124, 9, 9, 1, 7, 7, 1, 7, 7, 124, 124] 124 rigid atoms, others: [9, 10, 11, 12, 13, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 390 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003320 none O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 38, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 1, 1, 1, 1, 38, 38, 124, 124, 124, 124, 124, 124, 1, 1] 124 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003320 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003320/1 /scratch/stefan/7769584/working/building/REAL300000003320 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/356 `/scratch/stefan/7769584/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1) `REAL300000003320.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003320 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 52, 56, 52, 56, 56, 52, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 56, 56, 56, 56, 52, 23, 7, 1, 1, 1, 1, 1, 56, 56] 56 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: 156 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003320 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [52, 36, 52, 36, 52, 52, 36, 6, 6, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 52, 52, 52, 51, 35, 6, 1, 7, 7, 1, 7, 7, 52, 52] 56 rigid atoms, others: [9, 10, 11, 12, 13, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000003320 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=NO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 49, 49, 49, 53, 53, 49, 53, 53, 49, 49, 1, 1, 1, 1, 9, 33, 49, 53, 53, 49, 53, 53, 1, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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/7769584/working/building/REAL300000003320 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003320 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003320/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003320/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003320 Building REAL300000003321 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003321' /scratch/stefan/7769584/working/building/REAL300000003321 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003321 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003321/0 /scratch/stefan/7769584/working/building/REAL300000003321 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/357 `/scratch/stefan/7769584/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1) `REAL300000003321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003321 none NC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 32, 32, 98, 102, 102, 98, 102, 102, 102, 102, 102, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 32, 98, 102, 102, 102, 102, 5, 1, 1, 1, 1, 1] 102 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 276 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003321 none NC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 66, 34, 34, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 66, 66, 66, 66, 102, 102, 87, 102, 102, 66, 66, 34, 7, 1, 1, 1, 1, 66, 102, 102, 102, 102, 102] 102 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 255 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: REAL300000003321 none NC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 52, 66, 66, 52, 61, 65, 66, 66, 66, 1, 1, 1, 1, 5, 5, 2, 5, 5, 1, 1, 9, 51, 66, 66, 66, 66, 1, 5, 5, 3, 5, 5] 102 rigid atoms, others: [0, 1, 2, 3, 32, 15, 16, 17, 18, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 229 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003321 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003321 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003321/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003321 Building REAL300000003322 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003322' /scratch/stefan/7769584/working/building/REAL300000003322 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003322 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003322/0 /scratch/stefan/7769584/working/building/REAL300000003322 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/358 `/scratch/stefan/7769584/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003322 none CCC(=O)NC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 172, 172, 74, 45, 148, 148, 29, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 201, 172, 148, 148, 29, 29, 29, 5, 1, 1, 1, 1, 148, 148] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 828 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: REAL300000003322 none CCC(=O)NC1=CC=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 72, 148, 148, 90, 145, 148, 148, 148, 148, 1, 1, 39, 39, 39, 39, 39, 5, 1, 1, 13, 13, 13, 72, 148, 148, 148, 148, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 41, 22, 23, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 653 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003322 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003322 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003322/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003322 Building REAL300000003323 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003323' /scratch/stefan/7769584/working/building/REAL300000003323 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003323 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003323/0 /scratch/stefan/7769584/working/building/REAL300000003323 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/359 `/scratch/stefan/7769584/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(C)=C2S1) `REAL300000003323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003323 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 36, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 44, 44, 44, 44, 2, 2, 2, 1, 1, 1, 2, 2, 2] 44 rigid atoms, others: [1, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003323 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 6, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003323 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003323/1 /scratch/stefan/7769584/working/building/REAL300000003323 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/360 `/scratch/stefan/7769584/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(C)C=CC=C12) `REAL300000003323.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003323 none CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(C)C=CC=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 15, 5, 15, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 15, 15, 15, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 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: 67 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: REAL300000003323 none CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(C)C=CC=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 24, 24, 25, 25, 24, 24, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 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, 32, 33, 34, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003323 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003323 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003323/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003323/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003323 Building REAL300000003324 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003324' /scratch/stefan/7769584/working/building/REAL300000003324 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003324 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003324/0 /scratch/stefan/7769584/working/building/REAL300000003324 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/361 `/scratch/stefan/7769584/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1) `REAL300000003324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003324 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 141, 141, 129, 51, 51, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 141, 141, 141, 141, 129, 51, 12, 12, 1, 1, 1, 1, 141, 141] 141 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003324 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 56, 89, 89, 49, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 89, 89, 89, 89, 49, 8, 1, 1, 12, 12, 12, 12, 89, 89] 141 rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) 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: REAL300000003324 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 40, 40, 90, 90, 90, 90, 141, 141, 141, 141, 141, 141, 141, 141, 90, 1, 1, 1, 1, 7, 40, 90, 90, 141, 141, 141, 141, 1, 1] 141 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003324 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003324 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003324/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003324 Building REAL300000003325 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003325' /scratch/stefan/7769584/working/building/REAL300000003325 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003325 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003325/0 /scratch/stefan/7769584/working/building/REAL300000003325 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/362 `/scratch/stefan/7769584/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1) `REAL300000003325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003325 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 5, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 38, 45, 45, 38, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 38, 45, 45, 45, 45, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2] 45 rigid atoms, others: [1, 36, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 41, 42, 43]) total number of confs: 168 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003325 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 5, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 6, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 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: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003325 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003325/1 /scratch/stefan/7769584/working/building/REAL300000003325 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/363 `/scratch/stefan/7769584/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(C)C=C(C)C=C12) `REAL300000003325.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003325 none CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(C)C=C(C)C=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 5, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 5, 15, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 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: REAL300000003325 none CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(C)C=C(C)C=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 5, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 26, 26, 27, 27, 26, 26, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 27, 27, 27, 27, 2, 2, 2, 1, 2, 2, 2, 1] 27 rigid atoms, others: [0, 1, 2, 3, 39, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003325 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003325 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003325/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003325/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003325 Building REAL300000003326 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003326' /scratch/stefan/7769584/working/building/REAL300000003326 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003326 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003326/0 /scratch/stefan/7769584/working/building/REAL300000003326 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/364 `/scratch/stefan/7769584/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(C)(C)C)=N1) `REAL300000003326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003326 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 71, 71, 84, 84, 71, 71, 84, 84, 84, 84, 1, 1, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 13, 84, 84, 84, 84, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 104 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000003326 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 84, 84, 84, 84, 104, 104, 104, 84, 25, 25, 25, 25, 1, 1, 1, 1, 84, 104, 104, 104, 104, 104, 104, 104, 104, 104] 104 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003326 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003326/1 /scratch/stefan/7769584/working/building/REAL300000003326 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/365 `/scratch/stefan/7769584/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(C)(C)C)=N1) `REAL300000003326.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003326 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 27, 45, 45, 27, 27, 45, 46, 46, 45, 1, 1, 1, 1, 1, 4, 4, 4, 1, 8, 8, 8, 27, 45, 45, 46, 46, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 46 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 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: REAL300000003326 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CSC(C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 46, 46, 45, 45, 46, 46, 46, 45, 27, 27, 27, 6, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003326 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003326 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003326/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003326/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003326 Building REAL300000003327 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003327' /scratch/stefan/7769584/working/building/REAL300000003327 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003327 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003327/0 /scratch/stefan/7769584/working/building/REAL300000003327 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/366 `/scratch/stefan/7769584/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C2C=C(F)C(F)=C3Br)C=C1) `REAL300000003327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003327 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C2C=C(F)C(F)=C3Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 17, 1, 1, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 10, 7, 1, 1, 10, 10] 11 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003327 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=C2C=C(F)C(F)=C3Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 17, 1, 1, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 1, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003327 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003327 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003327/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003327 Building REAL300000003328 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003328' /scratch/stefan/7769584/working/building/REAL300000003328 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003328 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003328/0 /scratch/stefan/7769584/working/building/REAL300000003328 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/367 `/scratch/stefan/7769584/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003328 none CCN(C)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 81, 61, 81, 16, 61, 16, 48, 48, 16, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 48, 48, 120, 120, 120, 120, 120, 81, 81, 81, 48, 48, 16, 4, 1, 1, 1, 1, 48, 48] 120 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 567 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003328 none CCN(C)C(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 6, 6, 33, 48, 48, 33, 48, 48, 48, 48, 48, 1, 1, 21, 21, 21, 21, 21, 13, 13, 13, 1, 1, 6, 33, 48, 48, 48, 48, 1, 1] 120 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 5, 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]) total number of confs: 240 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003328 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003328 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003328/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003328 Building REAL300000003329 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003329' /scratch/stefan/7769584/working/building/REAL300000003329 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003329 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003329/0 /scratch/stefan/7769584/working/building/REAL300000003329 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/368 `/scratch/stefan/7769584/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C21) `REAL300000003329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003329 none CCN1CCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 29, 7, 1, 1, 1, 1, 44, 44] 44 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003329 none CCN1CCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 44, 44, 36, 44, 44, 44, 44, 44, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 10, 35, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 20, 21, 22, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003329 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003329/1 /scratch/stefan/7769584/working/building/REAL300000003329 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/369 `/scratch/stefan/7769584/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC2=CC(C=[NH+]NC3=CC=C(C(=O)[O-])C=C3)=CC=C21) `REAL300000003329.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003329 none CCN1CCC2=CC(C=[NH+]NC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 16, 16, 6, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 16, 6, 1, 1, 1, 1, 51, 51] 51 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 87 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: REAL300000003329 none CCN1CCC2=CC(C=[NH+]NC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 34, 51, 51, 50, 51, 51, 51, 51, 51, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 34, 51, 51, 51, 51, 1, 1] 51 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 41, 40, 21, 22, 23, 33, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003329 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003329 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003329/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003329/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003329 Building REAL300000003330 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003330' /scratch/stefan/7769584/working/building/REAL300000003330 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003330 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003330/0 /scratch/stefan/7769584/working/building/REAL300000003330 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/370 `/scratch/stefan/7769584/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(Cl)=C2S1) `REAL300000003330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003330 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(Cl)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 35, 41, 41, 39, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 35, 41, 41, 41, 41, 2, 2, 2, 1, 1, 1] 41 rigid atoms, others: [1, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003330 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C)C2=CC=CC(Cl)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 32, 32, 6, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003330 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003330/1 /scratch/stefan/7769584/working/building/REAL300000003330 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/371 `/scratch/stefan/7769584/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(Cl)C=CC=C12) `REAL300000003330.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003330 none CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(Cl)C=CC=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 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, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 18, 18, 1, 1, 1, 1, 26, 26, 26] 26 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 75 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: REAL300000003330 none CC1=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)SC2=C(Cl)C=CC=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 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, 6, 6, 25, 25, 26, 26, 25, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 26, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 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, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003330 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003330 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003330/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003330/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003330 Building REAL300000003331 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003331' /scratch/stefan/7769584/working/building/REAL300000003331 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003331 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003331/0 /scratch/stefan/7769584/working/building/REAL300000003331 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/372 `/scratch/stefan/7769584/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C) `REAL300000003331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003331 none CC(C)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 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, 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] 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: [24, 18, 24, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 31, 31, 51, 51, 51, 51, 24, 24, 24, 24, 24, 24, 24, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 51, 51, 51, 51, 51, 51, 51, 51, 51] 51 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 15, 16, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 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: REAL300000003331 none CC(C)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 12, 12, 18, 18, 12, 12, 18, 18, 18, 18, 1, 1, 1, 6, 6, 17, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 18, 18, 18, 18, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18] 51 rigid atoms, others: [19, 1, 34, 3, 4, 5, 6, 33, 41, 42, 17, 18, 35, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 111 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003331 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003331 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003331/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003331 Building REAL300000003332 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003332' /scratch/stefan/7769584/working/building/REAL300000003332 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003332 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003332/0 /scratch/stefan/7769584/working/building/REAL300000003332 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/373 `/scratch/stefan/7769584/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1O) `REAL300000003332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003332 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 33, 43, 43, 33, 33, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 33, 43, 43, 43, 43, 1, 2, 2, 2, 1, 2] 86 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35]) total number of confs: 181 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: REAL300000003332 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 43, 43, 43, 42, 43, 43, 43, 43, 21, 21, 21, 6, 1, 1, 1, 1, 43, 43, 43, 43, 43, 86] 86 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 166 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003332 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003332/1 /scratch/stefan/7769584/working/building/REAL300000003332 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/374 `/scratch/stefan/7769584/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Cl)=C1[O-]) `REAL300000003332.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003332 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 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, 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] 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, 3, 13, 21, 21, 13, 13, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 21, 21, 21, 21, 1, 2, 2, 2, 1] 21 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003332 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 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, 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] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 21, 21, 21, 21, 21] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 34 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003332 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003332 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003332/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003332/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003332 Building REAL300000003333 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003333' /scratch/stefan/7769584/working/building/REAL300000003333 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003333 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003333/0 /scratch/stefan/7769584/working/building/REAL300000003333 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/375 `/scratch/stefan/7769584/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl) `REAL300000003333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003333 none CSC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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: [97, 81, 66, 82, 82, 38, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 83, 83, 97, 97, 97, 82, 82, 38, 6, 1, 1, 1, 1, 83] 97 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003333 none CSC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 1, 1, 1, 12, 12, 56, 82, 82, 56, 56, 82, 82, 82, 82, 1, 1, 1, 7, 7, 7, 1, 1, 12, 56, 82, 82, 82, 82, 1] 97 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003333 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003333 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003333/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003333 Building REAL300000003334 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003334' /scratch/stefan/7769584/working/building/REAL300000003334 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003334 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003334/0 /scratch/stefan/7769584/working/building/REAL300000003334 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/376 `/scratch/stefan/7769584/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1CCCC(N=NC1=CC=C(C(=O)[O-])C=C1)C2) `REAL300000003334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003334 none COC1=CC=CC2=C1CCCC(N=NC1=CC=C(C(=O)[O-])C=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12] 12 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) 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: REAL300000003334 none COC1=CC=CC2=C1CCCC(N=NC1=CC=C(C(=O)[O-])C=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 12, 10, 10, 12, 12, 12, 12, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1] 12 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42] set([0, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003334 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003334 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003334/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003334 Building REAL300000003335 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003335' /scratch/stefan/7769584/working/building/REAL300000003335 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003335 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003335/0 /scratch/stefan/7769584/working/building/REAL300000003335 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/377 `/scratch/stefan/7769584/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl) `REAL300000003335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003335 none CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 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, 35, 39, 39, 20, 20, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 20, 6, 1, 1, 1, 1, 39, 39, 39] 39 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 90 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003335 none CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 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, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 30, 39, 39, 31, 39, 39, 39, 39, 39, 1, 1, 3, 3, 4, 4, 4, 4, 1, 1, 10, 30, 39, 39, 39, 39, 1, 1, 4] 39 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 36, 28, 29, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003335 none CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 17, 31, 39, 39, 31, 39, 39, 39, 39, 39, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 12, 30, 39, 39, 39, 39, 4, 4, 1] 39 rigid atoms, others: [0, 1, 2, 3, 4, 38, 22, 23, 24] set([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, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003335 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003335 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003335/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003335 Building REAL300000003336 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003336' /scratch/stefan/7769584/working/building/REAL300000003336 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003336 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003336/0 /scratch/stefan/7769584/working/building/REAL300000003336 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/378 `/scratch/stefan/7769584/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(C)=C2)C=C1) `REAL300000003336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003336 none CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(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', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 38, 40, 40, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 65, 65, 65, 65, 65, 40, 40, 27, 6, 1, 1, 1, 1, 40, 40, 40, 40, 65, 65] 65 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003336 none CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(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', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 10, 10, 36, 40, 40, 36, 36, 40, 40, 40, 40, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 10, 36, 40, 40, 40, 40, 2, 2, 2, 1, 7, 7] 65 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 20, 21, 22, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003336 none CC1=NN(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(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', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 1, 2, 22, 23, 57, 65, 65, 57, 57, 65, 65, 65, 65, 7, 7, 7, 1, 1, 2, 2, 2, 7, 7, 21, 57, 65, 65, 65, 65, 7, 7, 7, 7, 1, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003336 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003336 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003336/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003336 Building REAL300000003337 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003337' /scratch/stefan/7769584/working/building/REAL300000003337 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003337 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003337/0 /scratch/stefan/7769584/working/building/REAL300000003337 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/379 `/scratch/stefan/7769584/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)C(F)(F)F)C=C2)C=C1) `REAL300000003337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003337 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)C(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [26, 23, 26, 21, 26, 26, 21, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 26, 26, 26, 26, 21, 6, 1, 1, 1, 1, 26, 26] 49 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000003337 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)C(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 23, 23, 26, 26, 23, 24, 49, 49, 49, 49, 49, 49, 26, 26, 1, 1, 1, 1, 8, 23, 26, 26, 26, 26, 1, 1] 49 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003337 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003337 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003337/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003337 Building REAL300000003338 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003338' /scratch/stefan/7769584/working/building/REAL300000003338 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003338 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003338/0 /scratch/stefan/7769584/working/building/REAL300000003338 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/380 `/scratch/stefan/7769584/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003338 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 36, 36, 69, 69, 69, 69, 69, 44, 44, 28, 28, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 44, 44, 44, 44, 69, 69, 44, 44, 28, 7, 1, 1, 1, 1] 69 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 154 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003338 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 23, 23, 59, 69, 69, 59, 68, 69, 69, 69, 69, 7, 7, 7, 7, 1, 1, 7, 7, 23, 59, 69, 69, 69, 69] 69 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000003338 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 12, 12, 38, 44, 44, 38, 44, 44, 44, 44, 44, 2, 2, 2, 1, 7, 7, 1, 1, 12, 38, 44, 44, 44, 44] 69 rigid atoms, others: [0, 1, 2, 3, 4, 32, 10, 11, 12, 13, 28, 31] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003338 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003338 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003338/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003338 Building REAL300000003339 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003339' /scratch/stefan/7769584/working/building/REAL300000003339 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003339 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003339/0 /scratch/stefan/7769584/working/building/REAL300000003339 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/381 `/scratch/stefan/7769584/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003339 none CCNC(=O)C1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 168, 107, 168, 107, 107, 107, 107, 107, 38, 38, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 168, 107, 107, 107, 107, 38, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000003339 none CCNC(=O)C1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 10, 10, 56, 107, 107, 56, 57, 107, 107, 107, 107, 35, 35, 35, 35, 35, 11, 1, 1, 1, 1, 10, 56, 107, 107, 107, 107] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 4, 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: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003339 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003339 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003339/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003339 Building REAL300000003340 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003340' /scratch/stefan/7769584/working/building/REAL300000003340 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003340 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003340/0 /scratch/stefan/7769584/working/building/REAL300000003340 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/382 `/scratch/stefan/7769584/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1) `REAL300000003340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003340 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 108, 92, 27, 27, 7, 7, 7, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 92, 27, 7, 7, 7, 7, 1, 1, 1, 1, 108, 108] 108 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 262 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003340 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [91, 91, 91, 81, 91, 91, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 91, 91, 91, 91, 61, 11, 1, 1, 1, 1, 7, 7, 2, 7, 91, 91] 108 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003340 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 42, 42, 74, 74, 74, 74, 74, 74, 90, 90, 74, 90, 90, 90, 1, 1, 1, 1, 11, 42, 74, 74, 74, 74, 90, 90, 90, 90, 1, 1] 90 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003340 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003340 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003340/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003340 Building REAL300000003341 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003341' /scratch/stefan/7769584/working/building/REAL300000003341 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003341 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003341/0 /scratch/stefan/7769584/working/building/REAL300000003341 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/383 `/scratch/stefan/7769584/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003341 none CCC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 78, 77, 78, 78, 78, 39, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 99, 99, 99, 99, 99, 78, 39, 6, 1, 1, 1, 1] 99 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003341 none CCC1=CC(Br)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 53, 78, 78, 54, 69, 78, 78, 78, 78, 1, 7, 7, 7, 7, 7, 1, 12, 53, 78, 78, 78, 78] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003341 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003341 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003341/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003341 Building REAL300000003342 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003342' /scratch/stefan/7769584/working/building/REAL300000003342 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003342 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003342/0 /scratch/stefan/7769584/working/building/REAL300000003342 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/384 `/scratch/stefan/7769584/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC(N=NC2=CC=C(C(=O)[O-])C=C2)C12CCOCC2) `REAL300000003342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003342 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=C(C(=O)[O-])C=C2)C12CCOCC2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', '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, 1, 11, 11, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 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, 78, 61, 78, 20, 20, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 94, 94, 94, 94, 94, 94, 94, 94, 94, 61, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20] 94 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53]) 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: REAL300000003342 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=C(C(=O)[O-])C=C2)C12CCOCC2 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', '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, 1, 11, 11, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 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: [44, 34, 44, 44, 13, 7, 13, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 7, 1, 1, 1, 1, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1] 94 rigid atoms, others: [7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003342 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003342 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003342/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003342 Building REAL300000003343 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003343' /scratch/stefan/7769584/working/building/REAL300000003343 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003343 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003343/0 /scratch/stefan/7769584/working/building/REAL300000003343 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/385 `/scratch/stefan/7769584/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=C(C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)O2)N1) `REAL300000003343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003343 none COC(=O)C1=CC2=C(C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)O2)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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 4, 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, 26, 46, 26, 26, 26, 26, 26, 21, 21, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 46, 46, 46, 26, 26, 21, 7, 1, 1, 1, 1, 26] 46 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) 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: REAL300000003343 none COC(=O)C1=CC2=C(C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)O2)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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 7, 7, 7, 1, 1, 6, 19, 26, 26, 26, 26, 1] 46 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 22, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003343 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003343 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003343/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003343 Building REAL300000003344 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003344' /scratch/stefan/7769584/working/building/REAL300000003344 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003344 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003344/0 /scratch/stefan/7769584/working/building/REAL300000003344 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/386 `/scratch/stefan/7769584/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003344 none COCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 145, 76, 47, 47, 47, 46, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 145, 145, 47, 46, 21, 5, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003344 none COCCOC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [72, 46, 27, 10, 1, 1, 1, 1, 1, 1, 4, 4, 30, 46, 46, 30, 30, 46, 46, 46, 46, 1, 72, 72, 72, 46, 46, 27, 27, 1, 1, 4, 30, 46, 46, 46, 46] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003344 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003344/1 /scratch/stefan/7769584/working/building/REAL300000003344 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/387 `/scratch/stefan/7769584/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003344.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003344 none COCCOC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 167, 99, 65, 65, 65, 65, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 167, 167, 65, 65, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000003344 none COCCOC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 18, 13, 3, 1, 1, 1, 1, 1, 1, 8, 60, 60, 64, 64, 60, 60, 64, 64, 64, 64, 1, 28, 28, 28, 18, 18, 13, 13, 1, 1, 8, 8, 64, 64, 64, 64] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003344 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003344 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003344/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003344/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003344 Building REAL300000003345 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003345' /scratch/stefan/7769584/working/building/REAL300000003345 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003345 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003345/0 /scratch/stefan/7769584/working/building/REAL300000003345 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/388 `/scratch/stefan/7769584/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003345 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 38, 38, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 92, 92, 92, 92, 92, 92, 38, 7, 1, 1, 1, 1] 92 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 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: REAL300000003345 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 70, 92, 92, 70, 70, 92, 92, 92, 92, 3, 3, 3, 1, 1, 1, 12, 70, 92, 92, 92, 92] 92 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 27, 28] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003345 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003345 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003345/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003345 Building REAL300000003346 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003346' /scratch/stefan/7769584/working/building/REAL300000003346 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003346 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003346/0 /scratch/stefan/7769584/working/building/REAL300000003346 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/389 `/scratch/stefan/7769584/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1) `REAL300000003346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003346 none O=C([O-])C1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 8, 14, 14, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 8, 4, 1, 1, 1, 1, 14, 14] 14 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 32, 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: REAL300000003346 none O=C([O-])C1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 4, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 4, 13, 14, 14, 14, 14, 1, 1] 14 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003346 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003346 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003346/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003346 Building REAL300000003347 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003347' /scratch/stefan/7769584/working/building/REAL300000003347 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003347 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003347/0 /scratch/stefan/7769584/working/building/REAL300000003347 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/390 `/scratch/stefan/7769584/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCC1=CC=CC=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003347 none CC(CCCCC1=CC=CC=C1)N=NC1=CC=C(C(=O)[O-])C=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', '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, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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, 5, 30, 90, 119, 147, 199, 201, 201, 200, 201, 201, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 30, 30, 30, 96, 96, 119, 115, 156, 156, 197, 199, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 959 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: REAL300000003347 none CC(CCCCC1=CC=CC=C1)N=NC1=CC=C(C(=O)[O-])C=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', '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, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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: [63, 17, 12, 6, 3, 1, 1, 1, 1, 1, 1, 1, 65, 197, 197, 201, 201, 199, 201, 201, 201, 201, 201, 63, 65, 65, 64, 21, 21, 13, 13, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [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, 32, 33, 34, 40, 41, 42, 43]) total number of confs: 490 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003347 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003347 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003347/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003347 Building REAL300000003348 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003348' /scratch/stefan/7769584/working/building/REAL300000003348 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003348 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003348/0 /scratch/stefan/7769584/working/building/REAL300000003348 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/391 `/scratch/stefan/7769584/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN=C(CN=NC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003348 none CC(C)(C)C1=NN=C(CN=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 63, 73, 73, 63, 63, 63, 27, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 73, 73, 73, 73, 73, 73, 73, 73, 73, 27, 27, 1, 1, 1, 1] 73 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003348 none CC(C)(C)C1=NN=C(CN=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 50, 51, 63, 63, 51, 51, 63, 63, 63, 63, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 63, 63, 63, 63] 73 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003348 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003348 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003348/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003348 Building REAL300000003349 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003349' /scratch/stefan/7769584/working/building/REAL300000003349 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003349 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003349/0 /scratch/stefan/7769584/working/building/REAL300000003349 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/392 `/scratch/stefan/7769584/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2O)C=C1) `REAL300000003349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003349 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [37, 31, 38, 31, 37, 37, 31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 38, 38, 31, 12, 1, 1, 2, 37, 37] 76 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 139 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: REAL300000003349 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 8, 23, 38, 38, 76, 1, 1] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 136 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003349 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003349/1 /scratch/stefan/7769584/working/building/REAL300000003349 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/393 `/scratch/stefan/7769584/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2[O-])C=C1) `REAL300000003349.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003349 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 10, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 10, 10, 9, 3, 1, 1, 9, 9] 10 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) 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: REAL300000003349 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Br)C=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 6, 10, 10, 10, 1, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003349 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003349 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003349/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003349/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003349 Building REAL300000003350 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003350' /scratch/stefan/7769584/working/building/REAL300000003350 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003350 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003350/0 /scratch/stefan/7769584/working/building/REAL300000003350 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/394 `/scratch/stefan/7769584/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C)C(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003350 none CC1=NN(C(C)C)C(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 80, 80, 78, 78, 35, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 80, 80, 80, 80, 80, 80, 80, 78, 78, 78, 34, 6, 1, 1, 1, 1] 80 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 123 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: REAL300000003350 none CC1=NN(C(C)C)C(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 1, 1, 1, 1, 12, 12, 58, 78, 78, 58, 59, 78, 78, 78, 78, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 2, 2, 2, 12, 58, 78, 78, 78, 78] 80 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10] set([5, 6, 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: 326 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003350 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003350 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003350/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003350 Building REAL300000003351 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003351' /scratch/stefan/7769584/working/building/REAL300000003351 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003351 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003351/0 /scratch/stefan/7769584/working/building/REAL300000003351 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/395 `/scratch/stefan/7769584/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC(C)C)S1) `REAL300000003351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003351 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 58, 107, 107, 74, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 4, 7, 7, 1, 13, 13, 13, 58, 107, 107, 107, 107, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7] 149 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 381 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003351 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 36, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 107, 107, 107, 107, 147, 149, 149, 107, 36, 36, 36, 7, 1, 1, 1, 1, 107, 107, 147, 147, 149, 149, 149, 149, 149, 149, 149] 149 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 378 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003351 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003351/1 /scratch/stefan/7769584/working/building/REAL300000003351 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/396 `/scratch/stefan/7769584/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003351.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003351 none CC(C)CC1=CC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 193, 201, 142, 142, 142, 142, 39, 4, 39, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 201, 193, 193, 142, 142, 39, 39, 39, 39, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003351 none CC(C)CC1=CC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 7, 1, 1, 1, 1, 1, 1, 13, 13, 85, 85, 142, 142, 85, 85, 142, 142, 142, 142, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 13, 13, 13, 13, 142, 142, 142, 142] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003351 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003351 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003351/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003351/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003351 Building REAL300000003352 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003352' /scratch/stefan/7769584/working/building/REAL300000003352 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003352 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003352/0 /scratch/stefan/7769584/working/building/REAL300000003352 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/397 `/scratch/stefan/7769584/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=C(N1)SC(C=NNC1=CC=C(C(=O)[O-])C=C1)=C2) `REAL300000003352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003352 none COC(=O)C1=CC2=C(N1)SC(C=NNC1=CC=C(C(=O)[O-])C=C1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 33, 53, 33, 33, 33, 33, 33, 33, 22, 22, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 53, 53, 53, 33, 33, 22, 7, 1, 1, 1, 1, 33] 53 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 35]) 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: REAL300000003352 none COC(=O)C1=CC2=C(N1)SC(C=NNC1=CC=C(C(=O)[O-])C=C1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 33, 33, 32, 33, 33, 33, 33, 33, 1, 5, 5, 5, 1, 1, 8, 24, 33, 33, 33, 33, 1] 53 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 23, 27, 28] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003352 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003352 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003352/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003352 Building REAL300000003353 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003353' /scratch/stefan/7769584/working/building/REAL300000003353 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003353 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003353/0 /scratch/stefan/7769584/working/building/REAL300000003353 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/398 `/scratch/stefan/7769584/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1) `REAL300000003353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003353 none O=C([O-])C1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 13, 13, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 10, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 13 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 22, 23, 24, 25, 26, 36, 35]) total number of confs: 41 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: REAL300000003353 none O=C([O-])C1=CC=C(NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 24 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003353 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003353 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003353/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003353 Building REAL300000003354 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003354' /scratch/stefan/7769584/working/building/REAL300000003354 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003354 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003354/0 /scratch/stefan/7769584/working/building/REAL300000003354 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/399 `/scratch/stefan/7769584/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2)C=C1) `REAL300000003354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003354 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 42, 38, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 43, 42, 38, 10, 1, 1, 1, 42, 42] 43 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000003354 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 20, 20, 43, 43, 43, 21, 43, 43, 43, 1, 1, 1, 1, 10, 20, 43, 43, 43, 1, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003354 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003354 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003354/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003354 Building REAL300000003355 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003355' /scratch/stefan/7769584/working/building/REAL300000003355 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003355 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003355/0 /scratch/stefan/7769584/working/building/REAL300000003355 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/400 `/scratch/stefan/7769584/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003355 none CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 47, 47, 47, 47, 47, 47, 30, 30, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 47, 47, 47, 47, 30, 7, 1, 1, 1, 1, 77, 77, 77, 77] 77 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003355 none CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 47, 47, 36, 45, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 36, 47, 47, 47, 47, 5, 5, 5, 5] 77 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, 40, 41, 42, 43, 44]) 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: REAL300000003355 none CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C(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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 4, 5, 5, 5, 22, 22, 63, 77, 77, 63, 77, 77, 77, 77, 77, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 22, 63, 77, 77, 77, 77, 2, 2, 2, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003355 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003355 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003355/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003355 Building REAL300000003356 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003356' /scratch/stefan/7769584/working/building/REAL300000003356 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003356 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003356/0 /scratch/stefan/7769584/working/building/REAL300000003356 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/401 `/scratch/stefan/7769584/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN=C(CC(F)(F)F)S2)C=C1) `REAL300000003356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003356 none O=C([O-])C1=CC=C(NN=CC2=CN=C(CC(F)(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [84, 50, 84, 50, 84, 84, 49, 11, 11, 1, 1, 1, 1, 1, 1, 8, 9, 8, 9, 1, 84, 84, 84, 84, 49, 11, 1, 8, 8, 84, 84] 139 rigid atoms, others: [9, 10, 11, 12, 13, 14, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003356 none O=C([O-])C1=CC=C(NN=CC2=CN=C(CC(F)(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 45, 46, 87, 87, 86, 87, 139, 139, 139, 139, 87, 1, 1, 1, 1, 12, 45, 87, 139, 139, 1, 1] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003356 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003356 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003356/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003356 Building REAL300000003357 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003357' /scratch/stefan/7769584/working/building/REAL300000003357 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003357 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003357/0 /scratch/stefan/7769584/working/building/REAL300000003357 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/402 `/scratch/stefan/7769584/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1) `REAL300000003357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003357 none O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 42, 54, 42, 54, 54, 40, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 54, 54, 54, 54, 40, 12, 1, 1, 1, 54, 54] 54 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003357 none O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 8, 24, 53, 53, 53, 1, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003357 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003357 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003357/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003357 Building REAL300000003358 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003358' /scratch/stefan/7769584/working/building/REAL300000003358 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003358 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003358/0 /scratch/stefan/7769584/working/building/REAL300000003358 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/403 `/scratch/stefan/7769584/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=CSC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1) `REAL300000003358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003358 none COC1=CC=CC(C2=CSC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 201, 201, 59, 59, 59, 59, 12, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 59, 12, 12, 1, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 277 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003358 none COC1=CC=CC(C2=CSC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 9, 57, 57, 59, 59, 57, 57, 59, 59, 59, 59, 1, 13, 17, 17, 17, 12, 13, 13, 1, 8, 8, 59, 59, 59, 59, 13] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000003358 none COC1=CC=CC(C2=CSC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 13, 13, 13, 13, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 3, 3, 3, 1, 1, 1, 13, 61, 61, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24, 38, 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]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003358 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003358 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003358/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003358 Building REAL300000003359 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003359' /scratch/stefan/7769584/working/building/REAL300000003359 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003359 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003359/0 /scratch/stefan/7769584/working/building/REAL300000003359 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/404 `/scratch/stefan/7769584/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])C=C1) `REAL300000003359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003359 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 27, 27, 27, 27, 24, 6, 1, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000003359 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 7, 24, 24, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 7, 24, 27, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003359 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003359 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003359/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003359 Building REAL300000003360 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003360' /scratch/stefan/7769584/working/building/REAL300000003360 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003360 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003360/0 /scratch/stefan/7769584/working/building/REAL300000003360 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/405 `/scratch/stefan/7769584/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003360 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 2, 2, 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: [89, 89, 89, 89, 89, 89, 89, 89, 90, 90, 90, 90, 90, 90, 38, 38, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 89, 89, 89, 89, 89, 89, 90, 90, 90, 90, 38, 7, 1, 1, 1, 1, 89, 89] 90 rigid atoms, others: [39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003360 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 2, 2, 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: [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 81, 90, 90, 81, 90, 90, 90, 90, 90, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 30, 81, 90, 90, 90, 90, 6, 6] 90 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) 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: REAL300000003360 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 4, 6, 6, 1, 1, 13, 13, 63, 89, 89, 63, 76, 89, 89, 89, 89, 1, 1, 2, 2, 2, 1, 6, 6, 6, 6, 13, 63, 89, 89, 89, 89, 1, 1] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 44, 14, 15, 43, 27, 28] set([8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003360 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003360 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003360/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003360 Building REAL300000003361 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003361' /scratch/stefan/7769584/working/building/REAL300000003361 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003361 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003361/0 /scratch/stefan/7769584/working/building/REAL300000003361 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/406 `/scratch/stefan/7769584/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(O)=C1OC) `REAL300000003361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003361 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(O)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 39, 39, 39, 39, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 49, 49, 49, 49, 39, 39, 28, 6, 1, 1, 1, 1, 78, 49, 49, 49] 98 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 177 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: REAL300000003361 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(O)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 8, 8, 25, 39, 39, 25, 25, 39, 39, 39, 39, 1, 1, 1, 1, 4, 3, 3, 3, 1, 1, 8, 25, 39, 39, 39, 39, 2, 5, 5, 5] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003361 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003361 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003361/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003361 Building REAL300000003362 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003362' /scratch/stefan/7769584/working/building/REAL300000003362 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003362 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003362/0 /scratch/stefan/7769584/working/building/REAL300000003362 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/407 `/scratch/stefan/7769584/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)C=C1) `REAL300000003362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003362 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)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', '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', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 1, 6, 6, 33, 52, 52, 34, 47, 52, 52, 52, 52, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 33, 52, 52, 52, 52, 1, 1, 1, 1] 57 rigid atoms, others: [2, 35, 36, 37, 34, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 253 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: REAL300000003362 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)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', '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', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 30, 30, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 52, 52, 48, 49, 52, 52, 52, 52, 52, 46, 46, 46, 46, 46, 7, 1, 1, 1, 1, 52, 52, 52, 52] 57 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 12, 13, 30, 31] set([0, 1, 2, 3, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 204 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003362 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003362 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003362/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003362 Building REAL300000003363 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003363' /scratch/stefan/7769584/working/building/REAL300000003363 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003363 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003363/0 /scratch/stefan/7769584/working/building/REAL300000003363 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/408 `/scratch/stefan/7769584/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003363 none CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 191, 151, 191, 78, 16, 16, 41, 41, 16, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 41, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 78, 78, 41, 41, 16, 4, 1, 1, 1, 1, 41, 41] 201 rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48]) total number of confs: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003363 none CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 50, 50, 36, 20, 36, 4, 1, 1, 1, 1, 1, 1, 7, 7, 24, 41, 41, 24, 41, 41, 41, 41, 41, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 4, 4, 1, 1, 7, 24, 41, 41, 41, 41, 1, 1] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003363 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003363 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003363/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003363 Building REAL300000003364 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003364' /scratch/stefan/7769584/working/building/REAL300000003364 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003364 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003364/0 /scratch/stefan/7769584/working/building/REAL300000003364 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/409 `/scratch/stefan/7769584/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C2COCCN2C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003364 none COC(=O)C1=C2COCCN2C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 71, 98, 71, 71, 71, 71, 71, 71, 71, 37, 37, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 71, 98, 98, 98, 71, 71, 71, 71, 71, 71, 37, 7, 1, 1, 1, 1, 71] 98 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003364 none COC(=O)C1=C2COCCN2C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 47, 71, 71, 64, 71, 71, 71, 71, 71, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 10, 47, 71, 71, 71, 71, 1] 98 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 24, 28, 29, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003364 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003364 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003364/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003364 Building REAL300000003365 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003365' /scratch/stefan/7769584/working/building/REAL300000003365 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003365 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003365/0 /scratch/stefan/7769584/working/building/REAL300000003365 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/410 `/scratch/stefan/7769584/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1) `REAL300000003365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003365 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 89, 98, 98, 87, 32, 32, 4, 7, 18, 18, 4, 1, 4, 1, 1, 1, 1, 1, 1, 18, 18, 98, 98, 98, 98, 87, 32, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 98, 98] 98 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 325 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003365 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 42, 61, 35, 61, 61, 35, 6, 6, 1, 1, 1, 1, 1, 1, 11, 11, 18, 18, 18, 18, 18, 1, 1, 61, 61, 61, 61, 34, 6, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 61, 61] 98 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 22, 23, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 289 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: REAL300000003365 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 20, 20, 29, 29, 20, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 1, 1, 1, 1, 7, 20, 29, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 29, 29, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003365 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003365 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003365/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003365 Building REAL300000003366 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003366' /scratch/stefan/7769584/working/building/REAL300000003366 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003366 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003366/0 /scratch/stefan/7769584/working/building/REAL300000003366 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/411 `/scratch/stefan/7769584/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003366 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 71, 71, 71, 71, 36, 36, 21, 21, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 36, 71, 71, 71, 36, 36, 21, 7, 1, 1, 1, 1] 71 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 131 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003366 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 25, 27, 63, 71, 71, 63, 63, 71, 71, 71, 71, 7, 7, 7, 7, 1, 1, 1, 7, 7, 23, 63, 71, 71, 71, 71] 71 rigid atoms, others: [3, 4, 5, 6, 7, 8, 28, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 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: REAL300000003366 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 12, 12, 28, 36, 36, 28, 28, 36, 36, 36, 36, 2, 2, 2, 1, 7, 7, 7, 1, 1, 12, 28, 36, 36, 36, 36] 71 rigid atoms, others: [0, 1, 2, 3, 4, 32, 9, 10, 11, 12, 27, 31] set([5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003366 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003366 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003366/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003366 Building REAL300000003367 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003367' /scratch/stefan/7769584/working/building/REAL300000003367 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003367 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003367/0 /scratch/stefan/7769584/working/building/REAL300000003367 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/412 `/scratch/stefan/7769584/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OCC1=CC=CC=C1) `REAL300000003367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003367 none CC(C)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OCC1=CC=CC=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 11, 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, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 68, 69, 68, 68, 68, 68, 200, 200, 201, 201, 200, 200, 201, 201, 201, 201, 68, 38, 20, 38, 3, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 68, 68, 68, 68, 201, 201, 201, 201, 68, 68, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 348 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003367 none CC(C)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OCC1=CC=CC=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 11, 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, 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, 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 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, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 41, 41, 70, 201, 201, 201, 201, 201, 201, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 694 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: REAL300000003367 none CC(C)C1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OCC1=CC=CC=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 11, 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, 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, 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 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, 12, 12, 21, 21, 12, 12, 21, 21, 21, 21, 1, 1, 1, 4, 4, 8, 34, 68, 68, 42, 68, 68, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 21, 21, 21, 21, 1, 1, 34, 34, 68, 68, 68, 68, 68] 201 rigid atoms, others: [1, 3, 4, 5, 38, 39, 44, 45, 17, 18, 19, 36, 6, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 359 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003367 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003367 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003367/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003367 Building REAL300000003368 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003368' /scratch/stefan/7769584/working/building/REAL300000003368 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003368 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003368/0 /scratch/stefan/7769584/working/building/REAL300000003368 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/413 `/scratch/stefan/7769584/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCCCC2C2=CC=CC=C2)C=C1) `REAL300000003368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003368 none O=C([O-])C1=CC=C(N=NC2CCCCCC2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 10 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003368 none O=C([O-])C1=CC=C(N=NC2CCCCCC2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 12 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003368 none O=C([O-])C1=CC=C(N=NC2CCCCCC2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 18 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003368 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003368 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003368/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003368 Building REAL300000003369 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003369' /scratch/stefan/7769584/working/building/REAL300000003369 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003369 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003369/0 /scratch/stefan/7769584/working/building/REAL300000003369 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/414 `/scratch/stefan/7769584/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C(Cl)=C2Cl)C=C1) `REAL300000003369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003369 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C(Cl)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 5, 15, 15, 15, 1, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 23, 23, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 17, 10, 1, 1, 23, 23] 23 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003369 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C(Cl)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 5, 15, 15, 15, 1, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 19, 20, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 9, 19, 23, 23, 1, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003369 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003369 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003369/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003369 Building REAL300000003370 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003370' /scratch/stefan/7769584/working/building/REAL300000003370 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003370 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003370/0 /scratch/stefan/7769584/working/building/REAL300000003370 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/415 `/scratch/stefan/7769584/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C2OCC(=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1) `REAL300000003370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003370 none CC1=CC(Cl)=C2OCC(=NNC3=CC=C(C(=O)[O-])C=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 12, 5, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 14] 14 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: REAL300000003370 none CC1=CC(Cl)=C2OCC(=NNC3=CC=C(C(=O)[O-])C=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 12, 5, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 7, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2, 1, 1, 1, 7, 14, 14, 14, 14, 1] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 20, 21, 25, 26, 27] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003370 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003370/1 /scratch/stefan/7769584/working/building/REAL300000003370 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/416 `/scratch/stefan/7769584/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C2OCC(N=NC3=CC=C(C(=O)[O-])C=C3)C2=C1) `REAL300000003370.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003370 none CC1=CC(Cl)=C2OCC(N=NC3=CC=C(C(=O)[O-])C=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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 12, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7] 7 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 12 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003370 none CC1=CC(Cl)=C2OCC(N=NC3=CC=C(C(=O)[O-])C=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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 12, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 20, 21, 25, 26, 27, 28] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 29, 30, 31]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003370 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003370 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003370/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003370/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003370 Building REAL300000003371 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003371' /scratch/stefan/7769584/working/building/REAL300000003371 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003371 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003371/0 /scratch/stefan/7769584/working/building/REAL300000003371 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/417 `/scratch/stefan/7769584/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C2=CC=C1Br) `REAL300000003371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003371 none CC1=C2NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C2=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 34, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 46, 33, 6, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003371 none CC1=C2NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C2=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 46, 46, 37, 37, 47, 47, 47, 47, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 8, 36, 46, 46, 47, 47, 1, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 22, 26, 27, 35] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003371 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003371/1 /scratch/stefan/7769584/working/building/REAL300000003371 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/418 `/scratch/stefan/7769584/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2NC=C(CN=NC3=CC=C(C(=O)[O-])C=C3)C2=CC=C1Br) `REAL300000003371.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003371 none CC1=C2NC=C(CN=NC3=CC=C(C(=O)[O-])C=C3)C2=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 2, 2, 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, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 12, 1, 1, 1, 1, 44, 44] 44 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003371 none CC1=C2NC=C(CN=NC3=CC=C(C(=O)[O-])C=C3)C2=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 2, 2, 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, 9, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 22, 26, 27, 35] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003371 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003371 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003371/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003371/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003371 Building REAL300000003372 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003372' /scratch/stefan/7769584/working/building/REAL300000003372 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003372 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003372/0 /scratch/stefan/7769584/working/building/REAL300000003372 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/419 `/scratch/stefan/7769584/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC(Br)=CC=C21) `REAL300000003372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003372 none CC1CCC(=NNC2=CC=C(C(=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 28 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: REAL300000003372 none CC1CCC(=NNC2=CC=C(C(=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 36, 37, 38] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 31]) total number of confs: 32 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003372 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003372 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003372/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003372 Building REAL300000003373 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003373' /scratch/stefan/7769584/working/building/REAL300000003373 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003373 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003373/0 /scratch/stefan/7769584/working/building/REAL300000003373 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/420 `/scratch/stefan/7769584/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1) `REAL300000003373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003373 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 79, 23, 23, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 79, 23, 12, 12, 1, 1, 82, 82] 82 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 203 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003373 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 36, 51, 51, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 51, 51, 51, 51, 33, 9, 1, 1, 12, 12, 51, 51] 82 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) 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: REAL300000003373 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 34, 34, 47, 47, 47, 47, 47, 64, 64, 64, 64, 64, 1, 1, 1, 1, 10, 34, 47, 47, 64, 64, 1, 1] 64 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003373 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003373 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003373/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003373 Building REAL300000003374 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003374' /scratch/stefan/7769584/working/building/REAL300000003374 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003374 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003374/0 /scratch/stefan/7769584/working/building/REAL300000003374 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/421 `/scratch/stefan/7769584/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003374 none COC(=O)CCC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 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, 158, 201, 138, 69, 69, 69, 69, 19, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 69, 201, 201, 201, 158, 158, 138, 138, 69, 69, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003374 none COC(=O)CCC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 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: [35, 35, 9, 35, 6, 1, 1, 1, 1, 1, 1, 7, 59, 59, 69, 69, 59, 60, 69, 69, 69, 69, 1, 35, 35, 35, 9, 9, 6, 6, 1, 1, 7, 7, 69, 69, 69, 69] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003374 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003374/1 /scratch/stefan/7769584/working/building/REAL300000003374 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/422 `/scratch/stefan/7769584/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003374.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003374 none COC(=O)CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [201, 201, 143, 201, 88, 25, 25, 25, 25, 18, 18, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 201, 201, 201, 143, 143, 88, 88, 25, 25, 18, 4, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 790 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003374 none COC(=O)CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [82, 82, 21, 82, 9, 1, 1, 1, 1, 1, 1, 4, 4, 14, 25, 25, 15, 15, 25, 25, 25, 25, 1, 82, 82, 82, 21, 21, 9, 9, 1, 1, 4, 14, 25, 25, 25, 25] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003374 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003374 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003374/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003374/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003374 Building REAL300000003375 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003375' /scratch/stefan/7769584/working/building/REAL300000003375 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003375 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003375/0 /scratch/stefan/7769584/working/building/REAL300000003375 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/423 `/scratch/stefan/7769584/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=C1) `REAL300000003375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003375 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 93, 93, 30, 40, 40, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 93, 93, 40, 40, 26, 6, 1, 1, 1, 1, 40] 93 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003375 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 32, 40, 40, 32, 32, 40, 40, 40, 40, 1, 1, 1, 5, 5, 1, 1, 8, 32, 40, 40, 40, 40, 1] 93 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 20, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003375 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003375 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003375/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003375 Building REAL300000003376 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003376' /scratch/stefan/7769584/working/building/REAL300000003376 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003376 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003376/0 /scratch/stefan/7769584/working/building/REAL300000003376 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/424 `/scratch/stefan/7769584/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=COC2=C(C)C=CC=C12) `REAL300000003376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003376 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=COC2=C(C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 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, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 42, 53, 53, 42, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 42, 53, 53, 53, 53, 1, 2, 2, 2, 1, 1, 1] 53 rigid atoms, others: [1, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 182 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003376 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=COC2=C(C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 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, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 53, 53, 53, 53, 53, 53, 53, 53, 53, 30, 30, 30, 6, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003376 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003376 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003376/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003376 Building REAL300000003377 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003377' /scratch/stefan/7769584/working/building/REAL300000003377 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003377 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003377/0 /scratch/stefan/7769584/working/building/REAL300000003377 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/425 `/scratch/stefan/7769584/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN=C(C3CCOCC3)O2)C=C1) `REAL300000003377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003377 none O=C([O-])C1=CC=C(NN=CC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 161, 184, 184, 161, 57, 56, 13, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 184, 184, 184, 184, 162, 57, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184] 184 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38]) total number of confs: 546 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003377 none O=C([O-])C1=CC=C(NN=CC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [87, 71, 87, 56, 87, 87, 56, 11, 11, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 87, 87, 87, 87, 56, 11, 1, 12, 13, 13, 12, 13, 12, 13, 13, 13, 87, 87] 184 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003377 none O=C([O-])C1=CC=C(NN=CC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 44, 44, 81, 81, 81, 81, 175, 175, 175, 175, 175, 81, 1, 1, 1, 1, 11, 44, 81, 175, 175, 175, 175, 175, 175, 175, 175, 175, 1, 1] 175 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003377 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003377/1 /scratch/stefan/7769584/working/building/REAL300000003377 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/426 `/scratch/stefan/7769584/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CN=C(C3CCOCC3)O2)C=C1) `REAL300000003377.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003377 none O=C([O-])C1=CC=C(N=NCC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 201, 201, 201, 76, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 76, 76, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38]) total number of confs: 421 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003377 none O=C([O-])C1=CC=C(N=NCC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [72, 72, 72, 59, 72, 72, 59, 59, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 72, 72, 72, 72, 9, 9, 1, 12, 12, 13, 12, 13, 12, 13, 12, 13, 72, 72] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000003377 none O=C([O-])C1=CC=C(N=NCC2=CN=C(C3CCOCC3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 23, 73, 73, 73, 73, 201, 201, 201, 201, 201, 73, 1, 1, 1, 1, 23, 23, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003377 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003377 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003377/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003377/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003377 Building REAL300000003378 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003378' /scratch/stefan/7769584/working/building/REAL300000003378 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003378 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003378/0 /scratch/stefan/7769584/working/building/REAL300000003378 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/427 `/scratch/stefan/7769584/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC=C2Br)C=C1) `REAL300000003378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003378 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 42, 38, 42, 42, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 38, 9, 1, 1, 1, 42, 42] 42 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 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: REAL300000003378 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 24, 42, 42, 42, 41, 42, 42, 42, 1, 1, 1, 1, 11, 23, 42, 42, 42, 1, 1] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003378 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003378 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003378/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003378 Building REAL300000003379 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003379' /scratch/stefan/7769584/working/building/REAL300000003379 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003379 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003379/0 /scratch/stefan/7769584/working/building/REAL300000003379 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/428 `/scratch/stefan/7769584/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1Cl) `REAL300000003379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003379 none CCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [45, 35, 9, 1, 9, 9, 53, 95, 95, 55, 78, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 35, 35, 53, 95, 95, 95, 95, 1, 1, 1, 1] 107 rigid atoms, others: [19, 34, 3, 36, 37, 15, 16, 17, 18, 35, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 599 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: REAL300000003379 none CCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [93, 80, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 95, 95, 58, 95, 95, 95, 93, 93, 93, 92, 92, 80, 80, 5, 1, 1, 1, 1, 95, 95, 57, 95] 107 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 504 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003379 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003379 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003379/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003379 Building REAL300000003380 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003380' /scratch/stefan/7769584/working/building/REAL300000003380 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003380 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003380/0 /scratch/stefan/7769584/working/building/REAL300000003380 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/429 `/scratch/stefan/7769584/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(Br)=C2F)C=C1) `REAL300000003380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003380 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(Br)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 15, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 23, 7, 1, 1, 26, 26] 26 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000003380 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(Br)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 15, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 9, 24, 26, 26, 1, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003380 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003380 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003380/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003380 Building REAL300000003381 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003381' /scratch/stefan/7769584/working/building/REAL300000003381 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003381 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003381/0 /scratch/stefan/7769584/working/building/REAL300000003381 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/430 `/scratch/stefan/7769584/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN=NC1=CC=C(C(=O)[O-])C=C1)N1C(=O)C2=CC=CC=C2C1=O) `REAL300000003381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003381 none CC(CN=NC1=CC=C(C(=O)[O-])C=C1)N1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 11, 11, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 21, 50, 50, 51, 51, 50, 50, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 21, 21, 51, 51, 51, 51, 1, 1, 1, 1] 51 rigid atoms, others: [1, 35, 36, 37, 38, 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, 32, 33, 34]) 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: REAL300000003381 none CC(CN=NC1=CC=C(C(=O)[O-])C=C1)N1C(=O)C2=CC=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 11, 11, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [50, 24, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 50, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 51, 51, 51, 51] 51 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 12, 13, 31] set([0, 1, 2, 3, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003381 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003381 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003381/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003381 Building REAL300000003382 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003382' /scratch/stefan/7769584/working/building/REAL300000003382 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003382 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003382/0 /scratch/stefan/7769584/working/building/REAL300000003382 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/431 `/scratch/stefan/7769584/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=C1) `REAL300000003382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003382 none COCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 35, 7, 1, 7, 7, 42, 69, 69, 42, 42, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 35, 35, 42, 69, 69, 69, 69, 1, 1, 1, 1] 89 rigid atoms, others: [32, 33, 34, 3, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 444 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: REAL300000003382 none COCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 74, 30, 30, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 69, 69, 30, 46, 69, 69, 86, 86, 86, 74, 74, 6, 1, 1, 1, 1, 69, 69, 69, 69] 89 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 429 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003382 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003382 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003382/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003382 Building REAL300000003383 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003383' /scratch/stefan/7769584/working/building/REAL300000003383 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003383 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003383/0 /scratch/stefan/7769584/working/building/REAL300000003383 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/432 `/scratch/stefan/7769584/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NN(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003383 none COC(=O)C1=NN(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 103, 137, 103, 103, 103, 102, 41, 40, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 137, 137, 137, 103, 103, 103, 40, 6, 1, 1, 1, 1, 103] 137 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003383 none COC(=O)C1=NN(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 12, 12, 67, 102, 102, 67, 67, 103, 102, 102, 102, 1, 13, 13, 13, 2, 2, 2, 12, 67, 103, 103, 102, 102, 1] 137 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 34, 21] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003383 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003383 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003383/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003383 Building REAL300000003384 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003384' /scratch/stefan/7769584/working/building/REAL300000003384 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003384 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003384/0 /scratch/stefan/7769584/working/building/REAL300000003384 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/433 `/scratch/stefan/7769584/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CN=NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1Br) `REAL300000003384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003384 none CC(C)(CN=NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 12, 44, 44, 44, 44, 1, 1, 1] 44 rigid atoms, others: [1, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 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: 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: REAL300000003384 none CC(C)(CN=NC1=CC=C(C(=O)[O-])C=C1)C1=C(F)C=CC=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [36, 10, 36, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 10, 10, 1, 1, 1, 1, 44, 44, 44] 44 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 13, 14, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003384 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003384 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003384/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003384 Building REAL300000003385 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003385' /scratch/stefan/7769584/working/building/REAL300000003385 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003385 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003385/0 /scratch/stefan/7769584/working/building/REAL300000003385 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/434 `/scratch/stefan/7769584/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1) `REAL300000003385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003385 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 26, 107, 107, 190, 201, 201, 190, 201, 201, 201, 201, 201, 26, 26, 26, 5, 1, 1, 1, 1, 26, 107, 107, 107, 190, 201, 201, 201, 201, 26, 26, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 33]) total number of confs: 568 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003385 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 72, 132, 132, 72, 84, 132, 132, 132, 132, 1, 1, 1, 1, 1, 7, 26, 26, 1, 13, 13, 13, 72, 132, 132, 132, 132, 1, 1, 7, 7, 26, 26, 26, 26, 26] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 669 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003385 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 132, 132, 132, 132, 175, 201, 201, 132, 31, 31, 31, 5, 1, 1, 1, 1, 132, 132, 175, 175, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 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: 528 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003385 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003385/1 /scratch/stefan/7769584/working/building/REAL300000003385 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/435 `/scratch/stefan/7769584/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1) `REAL300000003385.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003385 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 23, 107, 200, 200, 201, 201, 200, 200, 201, 201, 201, 201, 23, 23, 23, 5, 1, 1, 1, 1, 23, 107, 107, 107, 107, 201, 201, 201, 201, 23, 23, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 33]) total number of confs: 495 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003385 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 80, 80, 121, 121, 80, 80, 121, 121, 121, 121, 1, 1, 1, 1, 1, 8, 23, 23, 1, 13, 13, 13, 13, 121, 121, 121, 121, 1, 1, 8, 8, 23, 23, 23, 23, 23] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003385 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 121, 121, 121, 121, 174, 201, 201, 121, 29, 29, 29, 29, 1, 1, 1, 1, 121, 121, 174, 174, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 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: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003385 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003385 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003385/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003385/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003385 Building REAL300000003386 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003386' /scratch/stefan/7769584/working/building/REAL300000003386 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003386 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003386/0 /scratch/stefan/7769584/working/building/REAL300000003386 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/436 `/scratch/stefan/7769584/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C(C(C)(C)C)O1) `REAL300000003386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003386 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C(C(C)(C)C)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 4, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 28, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 66, 66, 66, 52, 52, 52, 52, 27, 5, 1, 1, 1, 1, 52, 66, 66, 66, 66, 66, 66, 66, 66, 66] 66 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 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: 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: REAL300000003386 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C(C(C)(C)C)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 4, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 41, 52, 52, 41, 41, 52, 52, 52, 52, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 10, 41, 52, 52, 52, 52, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 66 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003386 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003386 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003386/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003386 Building REAL300000003387 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003387' /scratch/stefan/7769584/working/building/REAL300000003387 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003387 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003387/0 /scratch/stefan/7769584/working/building/REAL300000003387 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/437 `/scratch/stefan/7769584/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CN(CC3=CC=CC=C3)N=N2)C=C1) `REAL300000003387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003387 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 77, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 77, 77, 19, 4, 4, 1, 1, 1, 1, 1, 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]) total number of confs: 438 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003387 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 55, 68, 68, 55, 55, 9, 1, 1, 1, 1, 1, 9, 19, 19, 13, 19, 19, 1, 1, 68, 68, 68, 68, 9, 9, 1, 9, 9, 19, 19, 17, 19, 19, 68, 68] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000003387 none O=C([O-])C1=CC=C(N=NCC2=CN(CC3=CC=CC=C3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 24, 73, 73, 73, 199, 201, 201, 201, 201, 201, 73, 73, 1, 1, 1, 1, 24, 24, 73, 199, 199, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003387 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003387 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003387/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003387 Building REAL300000003388 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003388' /scratch/stefan/7769584/working/building/REAL300000003388 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003388 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003388/0 /scratch/stefan/7769584/working/building/REAL300000003388 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/438 `/scratch/stefan/7769584/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CN=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003388 none CC1=CC(Br)=CN=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 25, 6, 1, 1, 1, 1] 42 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000003388 none CC1=CC(Br)=CN=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 36, 42, 42, 36, 36, 42, 42, 42, 42, 2, 2, 2, 1, 1, 9, 36, 42, 42, 42, 42] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/7769584/working/building/REAL300000003388 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003388/1 /scratch/stefan/7769584/working/building/REAL300000003388 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/439 `/scratch/stefan/7769584/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CN=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003388.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003388 none CC1=CC(Br)=CN=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 14, 14, 1, 1, 1, 1] 38 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003388 none CC1=CC(Br)=CN=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 7, 7, 38, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003388 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003388 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003388/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003388/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003388 Building REAL300000003389 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003389' /scratch/stefan/7769584/working/building/REAL300000003389 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003389 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003389/0 /scratch/stefan/7769584/working/building/REAL300000003389 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/440 `/scratch/stefan/7769584/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1C(=O)[O-]) `REAL300000003389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003389 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1C(=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 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, 105, 105, 105, 36, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 122, 122, 122, 122, 122, 105, 36, 6, 1, 1, 1, 1, 105, 105] 122 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000003389 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1C(=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 10, 10, 54, 105, 105, 54, 54, 105, 105, 105, 105, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 10, 54, 105, 105, 105, 105, 1, 1] 122 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003389 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003389 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003389/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003389 Building REAL300000003390 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003390' /scratch/stefan/7769584/working/building/REAL300000003390 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003390 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003390/0 /scratch/stefan/7769584/working/building/REAL300000003390 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/441 `/scratch/stefan/7769584/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=O)OC(C)(C)C) `REAL300000003390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003390 none CCC1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 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, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 37, 37, 62, 65, 65, 65, 29, 29, 29, 29, 29, 23, 23, 23, 23, 1, 1, 1, 1, 23, 23, 65, 65, 65, 65, 65, 65, 65, 65, 65] 65 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 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: REAL300000003390 none CCC1CC(N=NC2=CC=C(C(=O)[O-])C=C2)CN1C(=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 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, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 13, 13, 23, 23, 13, 13, 23, 22, 23, 23, 1, 1, 1, 5, 5, 14, 16, 16, 16, 3, 3, 3, 3, 3, 1, 1, 1, 1, 23, 23, 23, 23, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 65 rigid atoms, others: [32, 1, 2, 3, 4, 5, 38, 33, 39, 16, 17, 18, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003390 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003390 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003390/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003390 Building REAL300000003391 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003391' /scratch/stefan/7769584/working/building/REAL300000003391 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003391 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003391/0 /scratch/stefan/7769584/working/building/REAL300000003391 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/442 `/scratch/stefan/7769584/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(S(=O)(=O)C(F)F)=C2)C=C1) `REAL300000003391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003391 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(S(=O)(=O)C(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [134, 72, 134, 72, 134, 134, 72, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 1, 134, 134, 134, 134, 72, 12, 1, 1, 1, 18, 1, 135, 135] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 33, 34]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003391 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(S(=O)(=O)C(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 44, 45, 118, 118, 45, 118, 118, 143, 143, 143, 159, 159, 118, 1, 1, 1, 1, 12, 44, 118, 118, 45, 159, 117, 1, 1] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 551 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003391 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003391 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003391/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003391 Building REAL300000003392 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003392' /scratch/stefan/7769584/working/building/REAL300000003392 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003392 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003392/0 /scratch/stefan/7769584/working/building/REAL300000003392 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/443 `/scratch/stefan/7769584/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C) `REAL300000003392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003392 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 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, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 13, 66, 66, 143, 201, 201, 143, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 66, 66, 66, 143, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 720 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003392 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 50, 87, 87, 50, 68, 87, 87, 87, 87, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 10, 10, 10, 50, 87, 87, 87, 87, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2] 201 rigid atoms, others: [1, 33, 13, 14, 15, 16, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 383 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003392 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCOCC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 87, 87, 87, 201, 201, 201, 201, 201, 87, 87, 87, 34, 34, 34, 6, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 87, 87] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 462 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003392 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003392 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003392/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003392 Building REAL300000003393 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003393' /scratch/stefan/7769584/working/building/REAL300000003393 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003393 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003393/0 /scratch/stefan/7769584/working/building/REAL300000003393 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/444 `/scratch/stefan/7769584/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C1C) `REAL300000003393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003393 none CC1OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C1C 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 6, 1, 1, 1, 1, 39, 40, 40, 40, 40] 40 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) 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: REAL300000003393 none CC1OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2C1C 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 34, 39, 39, 35, 39, 39, 39, 39, 39, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 34, 39, 39, 39, 39, 1, 1, 2, 2, 2] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 36, 26, 27, 28, 35] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003393 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003393 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003393/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003393 Building REAL300000003394 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003394' /scratch/stefan/7769584/working/building/REAL300000003394 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003394 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003394/0 /scratch/stefan/7769584/working/building/REAL300000003394 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/445 `/scratch/stefan/7769584/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC(F)F) `REAL300000003394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003394 none CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC(F)F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 83, 85, 85, 50, 50, 50, 50, 50, 28, 5, 1, 1, 1, 1, 50, 85] 85 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003394 none CC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OC(F)F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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 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, 7, 7, 30, 50, 50, 30, 50, 50, 50, 50, 50, 1, 1, 1, 7, 35, 35, 2, 2, 2, 1, 1, 7, 30, 50, 50, 50, 50, 1, 35] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 17, 18, 19, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003394 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003394 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003394/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003394 Building REAL300000003395 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003395' /scratch/stefan/7769584/working/building/REAL300000003395 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003395 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003395/0 /scratch/stefan/7769584/working/building/REAL300000003395 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/446 `/scratch/stefan/7769584/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1) `REAL300000003395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003395 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 14, 18, 18, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 18, 18, 18, 18, 14, 6, 1, 1, 18, 18] 18 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003395 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 18, 18, 18, 16, 16, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 15, 18, 18, 1, 1] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003395 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003395 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003395/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003395 Building REAL300000003396 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003396' /scratch/stefan/7769584/working/building/REAL300000003396 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003396 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003396/0 /scratch/stefan/7769584/working/building/REAL300000003396 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/447 `/scratch/stefan/7769584/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NC(Br)=C2F)C=C1) `REAL300000003396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003396 none O=C([O-])C1=CC=C(NN=CC2=CC=NC(Br)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 25, 21, 25, 24, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 25, 25, 21, 6, 1, 1, 24, 24] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) 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: REAL300000003396 none O=C([O-])C1=CC=C(NN=CC2=CC=NC(Br)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 24, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 10, 22, 24, 24, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003396 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003396 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003396/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003396 Building REAL300000003397 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003397' /scratch/stefan/7769584/working/building/REAL300000003397 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003397 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003397/0 /scratch/stefan/7769584/working/building/REAL300000003397 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/448 `/scratch/stefan/7769584/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=C(F)C=CC(Cl)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003397 none NC1=C(F)C=CC(Cl)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 15, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 19, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 18, 6, 1, 1, 1, 1] 29 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26]) 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: REAL300000003397 none NC1=C(F)C=CC(Cl)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 15, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 9, 9, 26, 29, 29, 26, 29, 29, 29, 29, 29, 1, 1, 1, 1, 9, 26, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003397 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003397 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003397/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003397 Building REAL300000003398 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003398' /scratch/stefan/7769584/working/building/REAL300000003398 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003398 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003398/0 /scratch/stefan/7769584/working/building/REAL300000003398 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/449 `/scratch/stefan/7769584/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=C1O) `REAL300000003398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003398 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 6, 6, 36, 36, 135, 168, 168, 135, 141, 168, 168, 168, 168, 6, 1, 1, 1, 1, 6, 6, 15, 15, 15, 6, 36, 135, 168, 168, 168, 168, 6, 1, 1, 1, 1, 1, 12] 336 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 605 number of broken/clashed sets: 24 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003398 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [146, 115, 115, 115, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 168, 168, 115, 115, 146, 146, 146, 115, 37, 6, 1, 1, 1, 1, 115, 168, 168, 168, 168, 168, 230] 336 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 637 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: REAL300000003398 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C2CC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 69, 115, 115, 69, 75, 115, 115, 115, 115, 1, 1, 1, 6, 6, 1, 1, 3, 3, 3, 1, 12, 69, 115, 115, 115, 115, 1, 6, 6, 6, 6, 6, 2] 336 rigid atoms, others: [1, 2, 3, 4, 5, 34, 17, 18, 19, 22, 23, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 492 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003398 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003398 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003398/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003398 Building REAL300000003399 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003399' /scratch/stefan/7769584/working/building/REAL300000003399 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003399 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003399/0 /scratch/stefan/7769584/working/building/REAL300000003399 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/450 `/scratch/stefan/7769584/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1) `REAL300000003399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003399 none O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [53, 43, 53, 42, 53, 53, 42, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 42, 13, 1, 1, 2, 53, 53] 106 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 185 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: REAL300000003399 none O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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 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, 7, 27, 28, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 7, 27, 53, 53, 106, 1, 1] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 185 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003399 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003399/1 /scratch/stefan/7769584/working/building/REAL300000003399 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/451 `/scratch/stefan/7769584/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1) `REAL300000003399.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003399 none O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 8, 12, 12, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 8, 4, 1, 1, 12, 12] 12 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003399 none O=C([O-])C1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 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 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, 6, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 6, 11, 12, 12, 1, 1] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003399 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003399 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003399/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003399/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003399 Building REAL300000003400 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003400' /scratch/stefan/7769584/working/building/REAL300000003400 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003400 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003400/0 /scratch/stefan/7769584/working/building/REAL300000003400 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/452 `/scratch/stefan/7769584/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br) `REAL300000003400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003400 none CC1=NC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 18, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 24, 24, 24, 24, 18, 7, 1, 1, 1, 1, 24] 24 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003400 none CC1=NC(Cl)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 24, 24, 20, 24, 24, 24, 24, 24, 1, 1, 1, 2, 2, 2, 8, 20, 24, 24, 24, 24, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003400 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003400 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003400/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003400 Building REAL300000003401 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003401' /scratch/stefan/7769584/working/building/REAL300000003401 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003401 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003401/0 /scratch/stefan/7769584/working/building/REAL300000003401 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/453 `/scratch/stefan/7769584/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F) `REAL300000003401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003401 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 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: [39, 12, 1, 12, 12, 64, 81, 81, 64, 70, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 64, 81, 81, 81, 81, 1, 2, 2, 1, 1] 91 rigid atoms, others: [32, 2, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 399 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: REAL300000003401 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 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: [61, 30, 30, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 81, 81, 81, 81, 81, 81, 81, 61, 61, 61, 61, 61, 5, 1, 1, 1, 1, 81, 81, 81, 81, 81] 91 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 266 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003401 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003401/1 /scratch/stefan/7769584/working/building/REAL300000003401 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/454 `/scratch/stefan/7769584/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F) `REAL300000003401.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003401 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [15, 9, 1, 9, 34, 34, 47, 47, 39, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 9, 47, 47, 47, 47, 1, 2, 2, 1, 1] 49 rigid atoms, others: [32, 2, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) 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: REAL300000003401 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [30, 23, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 47, 47, 47, 47, 47, 47, 47, 34, 34, 34, 34, 34, 23, 1, 1, 1, 1, 47, 47, 47, 47, 47] 49 rigid atoms, others: [4, 5, 6, 7, 8, 9, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003401 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003401 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003401/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003401/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003401 Building REAL300000003402 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003402' /scratch/stefan/7769584/working/building/REAL300000003402 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003402 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003402/0 /scratch/stefan/7769584/working/building/REAL300000003402 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/455 `/scratch/stefan/7769584/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1S(C)(=O)=O) `REAL300000003402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003402 none CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [97, 97, 97, 97, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 97, 97, 104, 104, 104, 97, 97, 97, 97, 40, 7, 1, 1, 1, 1, 104, 104, 104] 104 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003402 none CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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] 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, 13, 13, 66, 97, 97, 82, 97, 97, 97, 97, 97, 1, 1, 9, 9, 9, 2, 2, 2, 1, 13, 66, 97, 97, 97, 97, 9, 9, 9] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003402 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003402 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003402/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003402 Building REAL300000003403 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003403' /scratch/stefan/7769584/working/building/REAL300000003403 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000003403 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003403/0 /scratch/stefan/7769584/working/building/REAL300000003403 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/456 `/scratch/stefan/7769584/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(F)(F)F)NN=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003403 none CC1=C(C(F)(F)F)NN=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 15, 15, 15, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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: [26, 27, 27, 27, 27, 27, 27, 27, 27, 22, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 21, 6, 1, 1, 1, 1] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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: REAL300000003403 none CC1=C(C(F)(F)F)NN=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 15, 15, 15, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 23, 26, 26, 24, 26, 26, 26, 26, 26, 2, 2, 2, 1, 6, 23, 26, 27, 26, 27] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 25] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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/7769584/working/building/REAL300000003403 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003403/1 /scratch/stefan/7769584/working/building/REAL300000003403 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/457 `/scratch/stefan/7769584/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(F)(F)F)NN=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003403.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003403 none CC1=C(C(F)(F)F)NN=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 15, 15, 15, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 15, 15, 1, 1, 1, 1] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27]) 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: REAL300000003403 none CC1=C(C(F)(F)F)NN=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 15, 15, 15, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 9, 9, 43, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 25] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003403 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `2' /scratch/stefan/7769584/working/building/REAL300000003403/2 /scratch/stefan/7769584/working/building/REAL300000003403 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 2 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/458 `/scratch/stefan/7769584/working/3D/458' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)NN=C1C(F)(F)F) `REAL300000003403.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000003403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003403 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)NN=C1C(F)(F)F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 6, 1, 1, 1, 1, 28] 28 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003403 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)NN=C1C(F)(F)F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 23, 28, 28, 23, 23, 28, 28, 28, 28, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 23, 28, 28, 28, 28, 1] 28 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003403 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003403 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 2: /scratch/stefan/7769584/working/building/REAL300000003403/2.* 1: /scratch/stefan/7769584/working/building/REAL300000003403/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003403/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003403 Building REAL300000003404 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003404' /scratch/stefan/7769584/working/building/REAL300000003404 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003404 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003404/0 /scratch/stefan/7769584/working/building/REAL300000003404 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/459 `/scratch/stefan/7769584/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F) `REAL300000003404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003404 none CCCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', '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', '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, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 58, 46, 12, 1, 12, 12, 74, 138, 138, 74, 74, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 84, 84, 60, 60, 46, 46, 74, 138, 138, 138, 138, 1, 2, 2, 1, 1] 201 rigid atoms, others: [4, 38, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 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, 39, 40]) total number of confs: 999 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: REAL300000003404 none CCCCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', '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', '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, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 100, 90, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 138, 138, 138, 138, 138, 138, 138, 134, 134, 134, 133, 133, 102, 102, 90, 90, 5, 1, 1, 1, 1, 138, 138, 138, 138, 138] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 677 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003404 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003404/1 /scratch/stefan/7769584/working/building/REAL300000003404 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/460 `/scratch/stefan/7769584/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F) `REAL300000003404.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003404 none CCCCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 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, 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 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [78, 48, 33, 11, 1, 11, 54, 54, 95, 95, 63, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 81, 86, 86, 86, 86, 47, 48, 35, 35, 11, 95, 95, 95, 95, 1, 2, 2, 1, 1] 191 rigid atoms, others: [4, 38, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 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, 39, 40]) total number of confs: 688 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: REAL300000003404 none CCCCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(N)=CC=C1F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 6, 6, 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, 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 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [145, 114, 84, 30, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 93, 95, 95, 95, 95, 95, 95, 148, 153, 152, 153, 153, 114, 110, 88, 88, 30, 1, 1, 1, 1, 95, 95, 95, 95, 95] 191 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 14, 15] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 826 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003404 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003404 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003404/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003404/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003404 Building REAL300000003405 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003405' /scratch/stefan/7769584/working/building/REAL300000003405 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003405 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003405/0 /scratch/stefan/7769584/working/building/REAL300000003405 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/461 `/scratch/stefan/7769584/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=CC=CN=C21) `REAL300000003405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003405 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 33, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 33, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003405 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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, 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] 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: [24, 24, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 24, 24, 6, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003405 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003405 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003405/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003405 Building REAL300000003406 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003406' /scratch/stefan/7769584/working/building/REAL300000003406 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003406 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003406/0 /scratch/stefan/7769584/working/building/REAL300000003406 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/462 `/scratch/stefan/7769584/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=NC=CC=C2C=C1) `REAL300000003406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003406 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=NC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 31, 50, 50, 31, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 31, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003406 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=NC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 5, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003406 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003406 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003406/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003406 Building REAL300000003407 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003407' /scratch/stefan/7769584/working/building/REAL300000003407 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003407 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003407/0 /scratch/stefan/7769584/working/building/REAL300000003407 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/463 `/scratch/stefan/7769584/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1) `REAL300000003407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003407 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 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, 3, 7, 7, 7, 7, 7, 7, 4, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 176, 176, 128, 98, 33, 33, 98, 98, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 98, 98, 176, 176, 176, 128, 128, 98, 98, 33, 7, 1, 1, 1, 1, 98, 98] 176 rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 582 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003407 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 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, 3, 7, 7, 7, 7, 7, 7, 4, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 27, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 63, 98, 98, 63, 76, 98, 98, 98, 98, 1, 1, 26, 26, 26, 7, 7, 1, 1, 12, 63, 98, 98, 98, 98, 1, 1] 176 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 40, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 412 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: REAL300000003407 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 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, 3, 7, 7, 7, 7, 7, 7, 4, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 26, 26, 26, 26, 26, 84, 84, 150, 176, 176, 150, 176, 176, 176, 176, 176, 26, 26, 1, 1, 1, 8, 8, 26, 26, 84, 150, 176, 176, 176, 176, 26, 26] 176 rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 564 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003407 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003407 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003407/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003407 Building REAL300000003408 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003408' /scratch/stefan/7769584/working/building/REAL300000003408 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003408 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003408/0 /scratch/stefan/7769584/working/building/REAL300000003408 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/464 `/scratch/stefan/7769584/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2COC3=C(Br)C=CC=C23)C=C1) `REAL300000003408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003408 none O=C([O-])C1=CC=C(NN=C2COC3=C(Br)C=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 7, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 7, 1, 1, 1, 1, 1, 14, 14] 14 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003408 none O=C([O-])C1=CC=C(NN=C2COC3=C(Br)C=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 1, 1] 14 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003408 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003408/1 /scratch/stefan/7769584/working/building/REAL300000003408 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/465 `/scratch/stefan/7769584/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2COC3=C(Br)C=CC=C32)C=C1) `REAL300000003408.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003408 none O=C([O-])C1=CC=C(N=NC2COC3=C(Br)C=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 29, 30]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003408 none O=C([O-])C1=CC=C(N=NC2COC3=C(Br)C=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003408 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003408 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003408/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003408/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003408 Building REAL300000003409 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003409' /scratch/stefan/7769584/working/building/REAL300000003409 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003409 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003409/0 /scratch/stefan/7769584/working/building/REAL300000003409 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/466 `/scratch/stefan/7769584/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC2=CC=CC=C2S1) `REAL300000003409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003409 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [43, 13, 45, 123, 123, 127, 127, 123, 125, 127, 127, 127, 127, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 127, 127, 127, 127, 13, 13, 13, 13, 1, 1, 1, 1, 1] 127 rigid atoms, others: [36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003409 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 79, 80, 127, 127, 127, 127, 127, 127, 127, 127, 30, 30, 30, 30, 1, 1, 1, 1, 80, 80, 80, 80, 127, 127, 127, 127, 127] 127 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003409 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003409 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003409/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003409 Building REAL300000003410 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003410' /scratch/stefan/7769584/working/building/REAL300000003410 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003410 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003410/0 /scratch/stefan/7769584/working/building/REAL300000003410 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/467 `/scratch/stefan/7769584/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(Br)=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003410 none CCOC1=CC(Br)=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 146, 146, 146, 63, 146, 146, 146, 146, 41, 40, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 146, 146, 40, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 605 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003410 none CCOC1=CC(Br)=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 92, 146, 146, 92, 96, 146, 146, 146, 146, 33, 33, 33, 33, 33, 1, 1, 13, 92, 146, 146, 146, 146] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003410 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003410 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003410/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003410 Building REAL300000003411 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003411' /scratch/stefan/7769584/working/building/REAL300000003411 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003411 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003411/0 /scratch/stefan/7769584/working/building/REAL300000003411 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/468 `/scratch/stefan/7769584/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Br)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003411 none CN1C=C(Br)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 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, 20, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 42, 42, 42, 42, 20, 20, 1, 1, 1, 1] 42 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24]) 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: REAL300000003411 none CN1C=C(Br)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 40, 40, 42, 42, 40, 40, 42, 42, 42, 42, 1, 2, 2, 2, 1, 8, 8, 42, 42, 42, 42] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003411 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003411/1 /scratch/stefan/7769584/working/building/REAL300000003411 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/469 `/scratch/stefan/7769584/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003411.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003411 none CN1C=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 2, 2, 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, 26, 26, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 26, 7, 1, 1, 1, 1] 40 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24]) 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: REAL300000003411 none CN1C=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 2, 2, 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, 10, 10, 37, 40, 40, 38, 40, 40, 40, 40, 40, 1, 2, 2, 2, 1, 10, 37, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003411 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003411 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003411/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003411/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003411 Building REAL300000003412 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003412' /scratch/stefan/7769584/working/building/REAL300000003412 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003412 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003412/0 /scratch/stefan/7769584/working/building/REAL300000003412 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/470 `/scratch/stefan/7769584/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(I)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003412 none CN1C=NC(I)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'I', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 18, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 19, 6, 1, 1, 1, 1] 20 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24]) 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: REAL300000003412 none CN1C=NC(I)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'I', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 18, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 20, 20, 17, 18, 20, 20, 20, 20, 2, 2, 2, 1, 4, 17, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003412 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003412 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003412/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003412 Building REAL300000003413 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003413' /scratch/stefan/7769584/working/building/REAL300000003413 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003413 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003413/0 /scratch/stefan/7769584/working/building/REAL300000003413 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/471 `/scratch/stefan/7769584/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1) `REAL300000003413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003413 none O=C([O-])C1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 20, 32, 32, 20, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 20, 7, 2, 1, 1, 1, 1, 1, 32, 32] 64 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 37, 24, 25, 26, 27, 28, 29, 30, 36]) 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: REAL300000003413 none O=C([O-])C1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 11, 24, 64, 32, 32, 32, 32, 32, 1, 1] 64 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003413 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003413 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003413/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003413 Building REAL300000003414 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003414' /scratch/stefan/7769584/working/building/REAL300000003414 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003414 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003414/0 /scratch/stefan/7769584/working/building/REAL300000003414 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/472 `/scratch/stefan/7769584/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1) `REAL300000003414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003414 none O=C([O-])C1=CC=C(NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 27, 68, 68, 22, 4, 4, 1, 4, 29, 43, 43, 41, 43, 43, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 22, 29, 29, 43, 43, 43, 43, 1, 1, 1, 1, 1, 68, 68] 189 rigid atoms, others: [34, 35, 36, 37, 38, 9, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 370 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003414 none O=C([O-])C1=CC=C(NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 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, 175, 189, 189, 125, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 22, 43, 43, 34, 43, 43, 189, 189, 189, 189, 125, 5, 5, 1, 1, 1, 1, 43, 43, 43, 43, 43, 189, 189] 189 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003414 none O=C([O-])C1=CC=C(NN=C(CC2=CC=NC=C2)C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 45, 45, 173, 190, 190, 190, 190, 190, 45, 78, 78, 63, 78, 78, 1, 1, 1, 1, 11, 173, 173, 190, 190, 190, 190, 78, 78, 78, 78, 78, 1, 1] 190 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 730 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003414 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003414 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003414/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003414 Building REAL300000003415 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003415' /scratch/stefan/7769584/working/building/REAL300000003415 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003415 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003415/0 /scratch/stefan/7769584/working/building/REAL300000003415 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/473 `/scratch/stefan/7769584/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(OCCF)C=C32)C=C1) `REAL300000003415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003415 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(OCCF)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 34, 1, 1, 24, 24, 24, 24, 7, 1, 1, 1, 20, 20, 34, 34, 1, 24, 24] 84 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 18, 19, 20, 23, 24, 25, 26, 27, 36, 37, 31]) total number of confs: 160 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: REAL300000003415 none O=C([O-])C1=CC=C(NN=C2C(=O)NC3=CC=C(OCCF)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 60, 74, 74, 26, 26, 1, 1, 1, 1, 8, 26, 26, 26, 74, 74, 74, 74, 26, 1, 1] 74 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 179 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003415 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003415 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003415/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003415 Building REAL300000003416 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003416' /scratch/stefan/7769584/working/building/REAL300000003416 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003416 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003416/0 /scratch/stefan/7769584/working/building/REAL300000003416 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/474 `/scratch/stefan/7769584/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=C1) `REAL300000003416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003416 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 6, 6, 2, 2, 1, 1, 1, 1, 1] 18 rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 36 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003416 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 16, 16, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 14, 15, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 48 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: REAL300000003416 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@@H+]1CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 16, 16, 12, 12, 16, 15, 16, 16, 1, 1, 1, 1, 4, 6, 6, 4, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 1, 1, 4, 4, 6, 6, 4, 6, 6] 18 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 40, 39, 34, 16, 17, 18, 19, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003416 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003416/1 /scratch/stefan/7769584/working/building/REAL300000003416 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/475 `/scratch/stefan/7769584/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=C1) `REAL300000003416.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003416 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 6, 6, 3, 3, 1, 1, 1, 1, 1] 20 rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 36 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003416 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 14, 15, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 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: REAL300000003416 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)C[N@H+]1CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 15, 15, 11, 11, 15, 15, 15, 15, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 4, 4, 6, 6, 6, 6, 6] 20 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 40, 39, 34, 16, 17, 18, 19, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 70 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003416 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003416 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003416/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003416/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003416 Building REAL300000003417 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003417' /scratch/stefan/7769584/working/building/REAL300000003417 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003417 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003417/0 /scratch/stefan/7769584/working/building/REAL300000003417 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/476 `/scratch/stefan/7769584/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=NC=C2Cl)C=C1) `REAL300000003417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003417 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=NC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 16, 8, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 22, 25, 25, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 22, 8, 1, 1, 25, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003417 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=NC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 16, 8, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 19, 19, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 19, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003417 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003417 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003417/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003417 Building REAL300000003418 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003418' /scratch/stefan/7769584/working/building/REAL300000003418 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003418 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003418/0 /scratch/stefan/7769584/working/building/REAL300000003418 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/477 `/scratch/stefan/7769584/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2NC(C)=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1) `REAL300000003418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003418 none COC1=CC=C2NC(C)=C(C=NNC3=CC=C(C(=O)[O-])C=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.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 100, 100, 100, 100, 100, 100, 100, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 100, 100, 101, 101, 101, 100, 100, 100, 100, 100, 100, 40, 7, 1, 1, 1, 1, 100] 101 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) 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: REAL300000003418 none COC1=CC=C2NC(C)=C(C=NNC3=CC=C(C(=O)[O-])C=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.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 67, 100, 100, 73, 100, 100, 100, 100, 100, 1, 1, 3, 3, 3, 1, 1, 1, 2, 2, 2, 12, 67, 100, 100, 100, 100, 1] 101 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 22, 23, 27, 28, 29] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003418 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003418/1 /scratch/stefan/7769584/working/building/REAL300000003418 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/478 `/scratch/stefan/7769584/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2NC(C)=C(CN=NC3=CC=C(C(=O)[O-])C=C3)C2=C1) `REAL300000003418.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003418 none COC1=CC=C2NC(C)=C(CN=NC3=CC=C(C(=O)[O-])C=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.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 65, 65, 65, 65, 65, 65, 65, 65, 19, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 65, 65, 67, 67, 67, 65, 65, 65, 65, 65, 65, 19, 19, 1, 1, 1, 1, 65] 67 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) 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: REAL300000003418 none COC1=CC=C2NC(C)=C(CN=NC3=CC=C(C(=O)[O-])C=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.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 52, 53, 65, 65, 53, 53, 65, 65, 65, 65, 1, 1, 3, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 65, 65, 65, 65, 1] 67 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 22, 23, 27, 28, 29] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 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 /scratch/stefan/7769584/working/building/REAL300000003418 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003418 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003418/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003418/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003418 Building REAL300000003419 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003419' /scratch/stefan/7769584/working/building/REAL300000003419 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003419 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003419/0 /scratch/stefan/7769584/working/building/REAL300000003419 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/479 `/scratch/stefan/7769584/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C) `REAL300000003419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003419 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [74, 13, 74, 74, 154, 182, 182, 159, 182, 182, 182, 182, 182, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 74, 74, 74, 154, 182, 182, 182, 182, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 182 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003419 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 60, 118, 118, 63, 82, 118, 118, 118, 118, 1, 1, 1, 1, 13, 13, 13, 1, 1, 1, 10, 10, 10, 60, 118, 118, 118, 118, 1, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2] 182 rigid atoms, others: [1, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003419 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2CCC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 118, 118, 118, 182, 182, 182, 118, 118, 118, 38, 38, 38, 6, 1, 1, 1, 1, 118, 182, 182, 182, 182, 182, 182, 182, 118, 118, 118] 182 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003419 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003419 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003419/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003419 Building REAL300000003420 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003420' /scratch/stefan/7769584/working/building/REAL300000003420 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003420 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003420/0 /scratch/stefan/7769584/working/building/REAL300000003420 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/480 `/scratch/stefan/7769584/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1) `REAL300000003420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003420 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 85, 85, 85, 85, 85, 39, 39, 57, 57, 25, 25, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 57, 57, 85, 109, 109, 85, 85, 85, 57, 57, 25, 7, 1, 1, 1, 1, 57, 57, 85] 109 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003420 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 39, 57, 57, 40, 48, 57, 57, 57, 57, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 39, 57, 57, 57, 57, 1, 1, 3] 109 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43]) 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: REAL300000003420 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 13, 64, 85, 85, 63, 77, 85, 85, 85, 85, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 64, 85, 85, 85, 85, 3, 3, 1] 109 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 43, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003420 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003420 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003420/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003420 Building REAL300000003421 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003421' /scratch/stefan/7769584/working/building/REAL300000003421 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003421 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003421/0 /scratch/stefan/7769584/working/building/REAL300000003421 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/481 `/scratch/stefan/7769584/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CS1) `REAL300000003421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003421 none CS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 71, 87, 87, 71, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 87, 87, 87, 32, 7, 1, 1, 1, 1, 71, 71] 87 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000003421 none CS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 10, 1, 1, 1, 10, 10, 44, 71, 71, 44, 44, 71, 71, 71, 71, 1, 1, 1, 10, 10, 10, 10, 44, 71, 71, 71, 71, 1, 1] 87 rigid atoms, others: [1, 4, 5, 6, 18, 19, 20, 30, 31] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003421 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003421 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003421/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003421 Building REAL300000003422 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003422' /scratch/stefan/7769584/working/building/REAL300000003422 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003422 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003422/0 /scratch/stefan/7769584/working/building/REAL300000003422 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/482 `/scratch/stefan/7769584/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN2N=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2C1) `REAL300000003422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003422 none CC(C)(C)OC(=O)N1CCN2N=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2C1 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.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 58, 84, 58, 58, 58, 58, 58, 58, 30, 30, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 143, 143, 143, 143, 143, 143, 143, 143, 143, 58, 58, 58, 58, 58, 30, 7, 1, 1, 1, 1, 58, 58] 143 rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49]) 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: REAL300000003422 none CC(C)(C)OC(=O)N1CCN2N=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2C1 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.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 13, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 44, 58, 58, 44, 53, 58, 58, 58, 58, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 7, 44, 58, 58, 58, 58, 1, 1] 143 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 14, 48, 40, 49, 41, 26, 27, 5] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003422 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003422 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003422/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003422 Building REAL300000003423 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003423' /scratch/stefan/7769584/working/building/REAL300000003423 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003423 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003423/0 /scratch/stefan/7769584/working/building/REAL300000003423 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/483 `/scratch/stefan/7769584/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003423 none CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=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.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 191, 154, 191, 75, 27, 27, 27, 27, 18, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 75, 75, 27, 26, 17, 3, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003423 none CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=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.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 85, 47, 85, 9, 1, 1, 1, 1, 1, 1, 4, 4, 14, 26, 26, 14, 14, 26, 26, 26, 26, 1, 102, 102, 102, 102, 102, 102, 102, 102, 102, 47, 9, 9, 1, 1, 4, 14, 27, 27, 26, 26] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003423 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003423 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003423/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003423 Building REAL300000003424 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003424' /scratch/stefan/7769584/working/building/REAL300000003424 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003424 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003424/0 /scratch/stefan/7769584/working/building/REAL300000003424 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/484 `/scratch/stefan/7769584/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=N1) `REAL300000003424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003424 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 33, 33, 124, 144, 144, 124, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 33, 124, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 1, 1, 1] 144 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003424 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 44, 43, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 144, 144, 144, 144, 144, 100, 100, 100, 100, 100, 43, 6, 1, 1, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 144] 144 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 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: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003424 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2CCOCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 70, 100, 100, 70, 86, 100, 100, 100, 100, 1, 1, 7, 7, 7, 7, 7, 1, 2, 2, 2, 1, 13, 70, 100, 100, 100, 100, 7, 7, 7, 7, 7, 7, 7, 7, 7] 144 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003424 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003424 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003424/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003424 Building REAL300000003425 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003425' /scratch/stefan/7769584/working/building/REAL300000003425 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003425 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003425/0 /scratch/stefan/7769584/working/building/REAL300000003425 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/485 `/scratch/stefan/7769584/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1) `REAL300000003425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003425 none O=C([O-])C1=CC=C(NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 164, 180, 180, 153, 35, 35, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 180, 180, 180, 180, 153, 35, 5, 5, 1, 1, 1, 1, 5, 180, 180] 180 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 503 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003425 none O=C([O-])C1=CC=C(NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [117, 80, 117, 71, 117, 117, 69, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 117, 117, 117, 117, 69, 12, 1, 1, 5, 5, 5, 5, 1, 117, 117] 180 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 15, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003425 none O=C([O-])C1=CC=C(NN=CC2=CN=CC(C3=CC=CN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 42, 42, 118, 118, 118, 118, 118, 180, 180, 180, 180, 180, 118, 1, 1, 1, 1, 10, 42, 118, 118, 180, 180, 180, 180, 118, 1, 1] 180 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003425 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003425 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003425/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003425 Building REAL300000003426 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003426' /scratch/stefan/7769584/working/building/REAL300000003426 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003426 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003426/0 /scratch/stefan/7769584/working/building/REAL300000003426 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/486 `/scratch/stefan/7769584/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C(C)(C)C) `REAL300000003426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003426 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 4, 17, 26, 26, 17, 23, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 17, 26, 26, 26, 26, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 26 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003426 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=NN1C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 26, 26, 26, 26, 26, 26, 26, 26, 23, 23, 23, 5, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003426 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003426 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003426/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003426 Building REAL300000003427 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003427' /scratch/stefan/7769584/working/building/REAL300000003427 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003427 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003427/0 /scratch/stefan/7769584/working/building/REAL300000003427 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/487 `/scratch/stefan/7769584/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C2)C=C1) `REAL300000003427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003427 none O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 118, 52, 14, 3, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 118, 118, 118, 118, 52, 52, 3, 3, 1, 1, 1, 1, 1, 118, 118, 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: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003427 none O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 16, 8, 17, 17, 8, 8, 1, 1, 1, 1, 1, 9, 30, 69, 118, 118, 78, 118, 118, 1, 17, 17, 17, 17, 1, 1, 1, 1, 9, 9, 69, 69, 118, 118, 118, 118, 118, 1, 1, 17, 17] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 40, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) 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: REAL300000003427 none O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 77, 140, 201, 201, 201, 201, 201, 201, 26, 1, 1, 1, 1, 26, 26, 26, 26, 77, 77, 201, 201, 201, 201, 201, 201, 201, 26, 26, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003427 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003427 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003427/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003427 Building REAL300000003428 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003428' /scratch/stefan/7769584/working/building/REAL300000003428 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003428 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003428/0 /scratch/stefan/7769584/working/building/REAL300000003428 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/488 `/scratch/stefan/7769584/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCC3=CC(Cl)=CC=C3C2)C=C1) `REAL300000003428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003428 none O=C([O-])C1=CC=C(N=NC2CCC3=CC(Cl)=CC=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003428 none O=C([O-])C1=CC=C(N=NC2CCC3=CC(Cl)=CC=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003428 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003428 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003428/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003428 Building REAL300000003429 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003429' /scratch/stefan/7769584/working/building/REAL300000003429 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003429 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003429/0 /scratch/stefan/7769584/working/building/REAL300000003429 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/489 `/scratch/stefan/7769584/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NC3=C(CCCCC3)S2)C=C1) `REAL300000003429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003429 none O=C([O-])C1=CC=C(N=NCC2=NC3=C(CCCCC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 46, 47, 47, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 37, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003429 none O=C([O-])C1=CC=C(N=NCC2=NC3=C(CCCCC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 13, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 13, 13, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 36, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003429 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003429 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003429/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003429 Building REAL300000003430 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003430' /scratch/stefan/7769584/working/building/REAL300000003430 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003430 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003430/0 /scratch/stefan/7769584/working/building/REAL300000003430 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/490 `/scratch/stefan/7769584/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3C=C2O)C=C1) `REAL300000003430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003430 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 17, 6, 1, 1, 1, 1, 1, 1, 2, 22, 22] 44 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 35, 21, 22, 23, 24, 25, 26]) total number of confs: 53 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: REAL300000003430 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 20, 20, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 9, 20, 22, 22, 22, 22, 22, 22, 44, 1, 1] 44 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003430 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003430 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003430/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003430 Building REAL300000003431 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003431' /scratch/stefan/7769584/working/building/REAL300000003431 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003431 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003431/0 /scratch/stefan/7769584/working/building/REAL300000003431 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/491 `/scratch/stefan/7769584/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCC(=O)[O-]) `REAL300000003431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003431 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 77, 23, 23, 23, 12, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 93, 171, 184, 184, 111, 111, 111, 111, 111, 23, 11, 3, 1, 1, 1, 1, 23, 23, 171, 171] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 760 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003431 none CCOC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 10, 1, 1, 1, 1, 1, 7, 7, 15, 23, 23, 15, 15, 23, 23, 23, 23, 1, 1, 1, 1, 9, 46, 91, 91, 31, 31, 31, 31, 31, 1, 7, 15, 23, 23, 23, 23, 1, 1, 46, 46] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 38, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 472 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003431 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003431 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003431/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003431 Building REAL300000003432 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003432' /scratch/stefan/7769584/working/building/REAL300000003432 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003432 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003432/0 /scratch/stefan/7769584/working/building/REAL300000003432 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/492 `/scratch/stefan/7769584/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3CC3(F)F)N=C2)C=C1) `REAL300000003432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003432 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CC3(F)F)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 179, 179, 148, 52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 179, 179, 179, 179, 148, 52, 12, 1, 1, 1, 12, 179, 179] 179 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, 32]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003432 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CC3(F)F)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [84, 84, 84, 66, 84, 84, 52, 9, 9, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 83, 83, 84, 84, 52, 9, 1, 12, 12, 12, 1, 83, 83] 179 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 26, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003432 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CC3(F)F)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 1, 1, 1, 11, 46, 46, 82, 82, 82, 160, 160, 160, 160, 82, 82, 1, 1, 1, 1, 11, 46, 82, 160, 160, 160, 82, 1, 1] 160 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003432 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003432 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003432/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003432 Building REAL300000003433 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003433' /scratch/stefan/7769584/working/building/REAL300000003433 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003433 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003433/0 /scratch/stefan/7769584/working/building/REAL300000003433 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/493 `/scratch/stefan/7769584/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2C=C1) `REAL300000003433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003433 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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] 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: [11, 1, 11, 11, 35, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 35, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 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: REAL300000003433 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC2=CC=NC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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] 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: [24, 24, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 51, 51, 51, 51, 51, 51, 51, 51, 51, 24, 24, 24, 6, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003433 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003433 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003433/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003433 Building REAL300000003434 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003434' /scratch/stefan/7769584/working/building/REAL300000003434 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003434 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003434/0 /scratch/stefan/7769584/working/building/REAL300000003434 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/494 `/scratch/stefan/7769584/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1) `REAL300000003434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003434 none COC(=O)C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 155, 155, 155, 50, 42, 21, 21, 42, 42, 21, 21, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 42, 155, 201, 201, 201, 155, 155, 50, 50, 42, 42, 21, 6, 1, 1, 1, 1, 42, 42] 201 rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 506 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003434 none COC(=O)C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 18, 39, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 42, 42, 31, 31, 42, 42, 42, 42, 1, 1, 18, 39, 39, 39, 18, 18, 5, 5, 1, 1, 6, 31, 42, 42, 42, 42, 1, 1] 201 rigid atoms, others: [45, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 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, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 228 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: REAL300000003434 none COC(=O)C1=CC=C(COC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 51, 51, 127, 155, 155, 127, 145, 155, 155, 155, 155, 18, 18, 1, 8, 8, 8, 1, 1, 8, 8, 18, 18, 51, 127, 155, 155, 155, 155, 18, 18] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 28] set([0, 1, 3, 9, 10, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 512 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003434 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003434 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003434/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003434 Building REAL300000003435 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003435' /scratch/stefan/7769584/working/building/REAL300000003435 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003435 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003435/0 /scratch/stefan/7769584/working/building/REAL300000003435 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/495 `/scratch/stefan/7769584/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)S1) `REAL300000003435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003435 none CC1=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 14, 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, 2, 2, 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, 30, 30, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 47, 47, 47, 47, 47, 30, 7, 1, 1, 1, 1, 47, 47, 47] 47 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) 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: REAL300000003435 none CC1=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 14, 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, 2, 2, 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, 13, 13, 42, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 2, 2, 2, 13, 42, 47, 47, 47, 47, 2, 2, 2] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003435 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003435 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003435/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003435 Building REAL300000003436 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003436' /scratch/stefan/7769584/working/building/REAL300000003436 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003436 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003436/0 /scratch/stefan/7769584/working/building/REAL300000003436 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/496 `/scratch/stefan/7769584/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=C2)=N1) `REAL300000003436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003436 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 54, 167, 201, 201, 167, 170, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 54, 167, 201, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 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]) total number of confs: 677 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003436 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 44, 44, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 110, 110, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 44, 7, 1, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) 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: REAL300000003436 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 110, 110, 72, 73, 110, 110, 110, 110, 1, 1, 11, 11, 10, 11, 11, 11, 1, 2, 2, 2, 1, 12, 72, 110, 110, 110, 110, 11, 11, 10, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003436 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003436 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003436/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003436 Building REAL300000003437 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003437' /scratch/stefan/7769584/working/building/REAL300000003437 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003437 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003437/0 /scratch/stefan/7769584/working/building/REAL300000003437 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/497 `/scratch/stefan/7769584/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC(C3=CC=CC=C3Br)C2)C=C1) `REAL300000003437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003437 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=CC=C3Br)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 25, 25, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 25, 25, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 25, 25] 25 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003437 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=CC=C3Br)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 15, 13, 16, 16, 11, 11, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 16, 16, 16, 16, 1, 1, 1, 1, 7, 7, 1, 7, 1, 1, 16, 16] 25 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 19, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 30, 31, 34, 35]) total number of confs: 54 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: REAL300000003437 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=CC=C3Br)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 20, 20, 25, 25, 20, 25, 25, 25, 20, 1, 1, 1, 1, 20, 20, 20, 20, 25, 25, 21, 25, 20, 20, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003437 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003437 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003437/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003437 Building REAL300000003438 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003438' /scratch/stefan/7769584/working/building/REAL300000003438 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003438 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003438/0 /scratch/stefan/7769584/working/building/REAL300000003438 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/498 `/scratch/stefan/7769584/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)CC1=CC=CC=C1) `REAL300000003438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003438 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 22, 7, 22, 60, 60, 68, 68, 60, 60, 68, 68, 68, 68, 3, 8, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 21, 68, 68, 68, 68, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1] 68 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]) total number of confs: 250 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: REAL300000003438 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)CC1=CC=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 48, 47, 68, 68, 68, 68, 68, 68, 31, 31, 31, 31, 31, 21, 1, 1, 1, 1, 49, 49, 49, 49, 68, 68, 68, 68, 68, 68, 68] 68 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 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: 371 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003438 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003438 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003438/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003438 Building REAL300000003439 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003439' /scratch/stefan/7769584/working/building/REAL300000003439 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003439 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003439/0 /scratch/stefan/7769584/working/building/REAL300000003439 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/499 `/scratch/stefan/7769584/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCC3=CC=C(Br)C=C3C2)C=C1) `REAL300000003439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003439 none O=C([O-])C1=CC=C(N=NC2CCCC3=CC=C(Br)C=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 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: [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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003439 none O=C([O-])C1=CC=C(N=NC2CCCC3=CC=C(Br)C=C3C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 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: [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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003439 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003439 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003439/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003439 Building REAL300000003440 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003440' /scratch/stefan/7769584/working/building/REAL300000003440 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003440 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003440/0 /scratch/stefan/7769584/working/building/REAL300000003440 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/500 `/scratch/stefan/7769584/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CC3)S2)C=C1) `REAL300000003440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003440 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 174, 186, 186, 174, 87, 87, 29, 29, 29, 29, 5, 1, 1, 1, 1, 29, 186, 186, 186, 186, 174, 87, 29, 29, 5, 5, 1, 1, 1, 1, 1, 186, 186] 186 rigid atoms, others: [32, 33, 14, 15, 16, 17, 29, 30, 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, 34, 35]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003440 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [107, 69, 107, 65, 107, 107, 63, 12, 12, 1, 1, 1, 1, 1, 1, 8, 29, 29, 1, 107, 107, 107, 107, 63, 12, 1, 1, 8, 8, 29, 29, 29, 29, 29, 107, 107] 186 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003440 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 108, 108, 107, 108, 171, 187, 187, 108, 1, 1, 1, 1, 10, 45, 108, 108, 171, 171, 187, 187, 187, 187, 187, 1, 1] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 22, 35] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003440 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003440 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003440/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003440 Building REAL300000003441 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003441' /scratch/stefan/7769584/working/building/REAL300000003441 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003441 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003441/0 /scratch/stefan/7769584/working/building/REAL300000003441 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/501 `/scratch/stefan/7769584/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)(F)F)C=C2F)C=C1) `REAL300000003441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003441 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [69, 39, 70, 39, 70, 70, 39, 8, 8, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 1, 1, 1, 69, 69, 70, 70, 39, 8, 1, 1, 1, 69, 69] 124 rigid atoms, others: [9, 10, 11, 12, 13, 14, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003441 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 38, 39, 73, 73, 46, 73, 143, 143, 143, 143, 73, 73, 73, 1, 1, 1, 1, 7, 38, 72, 73, 73, 1, 1] 143 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003441 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003441 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003441/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003441 Building REAL300000003442 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003442' /scratch/stefan/7769584/working/building/REAL300000003442 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003442 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003442/0 /scratch/stefan/7769584/working/building/REAL300000003442 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/502 `/scratch/stefan/7769584/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)C(F)(F)F)=C2)C=C1) `REAL300000003442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003442 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [114, 72, 114, 72, 114, 114, 72, 12, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 114, 114, 114, 114, 72, 12, 1, 1, 1, 1, 115, 115] 175 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 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: REAL300000003442 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 32, 33, 65, 65, 33, 65, 65, 97, 97, 97, 97, 97, 97, 65, 1, 1, 1, 1, 10, 32, 65, 65, 33, 65, 1, 1] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 23, 24, 25, 26] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003442 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003442 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003442/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003442 Building REAL300000003443 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003443' /scratch/stefan/7769584/working/building/REAL300000003443 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003443 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003443/0 /scratch/stefan/7769584/working/building/REAL300000003443 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/503 `/scratch/stefan/7769584/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003443 none CC1=NC=CN1C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 131, 132, 34, 34, 34, 34, 24, 24, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 34, 34, 132, 132, 132, 132, 132, 34, 34, 24, 7, 1, 1, 1, 1, 34, 34, 34, 34] 132 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003443 none CC1=NC=CN1C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 30, 34, 34, 30, 30, 34, 34, 34, 34, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 12, 30, 34, 34, 34, 34, 2, 2, 2, 1] 132 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000003443 none CC1=NC=CN1C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 2, 25, 25, 103, 120, 116, 99, 97, 117, 119, 121, 121, 5, 5, 5, 2, 2, 2, 1, 1, 5, 5, 25, 103, 114, 112, 121, 121, 5, 5, 5, 5] 132 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003443 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003443 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003443/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003443 Building REAL300000003444 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003444' /scratch/stefan/7769584/working/building/REAL300000003444 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003444 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003444/0 /scratch/stefan/7769584/working/building/REAL300000003444 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/504 `/scratch/stefan/7769584/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)N(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1) `REAL300000003444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003444 none CC1=C(C)N(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 45, 49, 49, 26, 26, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 49, 75, 75, 75, 75, 75, 75, 75, 75, 49, 49, 26, 7, 1, 1, 1, 1, 49, 49, 75] 75 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003444 none CC1=C(C)N(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 12, 12, 35, 49, 49, 48, 49, 49, 49, 49, 49, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 12, 34, 49, 49, 49, 49, 1, 1, 3] 75 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 39, 40, 21, 22, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41]) 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: REAL300000003444 none CC1=C(C)N(C2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 13, 13, 49, 75, 75, 73, 74, 75, 75, 75, 75, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 13, 49, 75, 75, 75, 75, 3, 3, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003444 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003444 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003444/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003444 Building REAL300000003445 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003445' /scratch/stefan/7769584/working/building/REAL300000003445 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003445 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003445/0 /scratch/stefan/7769584/working/building/REAL300000003445 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/505 `/scratch/stefan/7769584/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1) `REAL300000003445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003445 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [129, 121, 122, 93, 119, 119, 80, 13, 13, 1, 1, 7, 7, 1, 1, 1, 1, 7, 7, 16, 16, 7, 119, 120, 119, 119, 80, 13, 7, 7, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 7, 119, 124] 145 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 454 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003445 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 61, 87, 87, 57, 9, 9, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 6, 6, 1, 87, 87, 87, 87, 57, 9, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 1, 87, 87] 145 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 17, 18, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 303 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: REAL300000003445 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 38, 38, 97, 97, 38, 38, 131, 131, 97, 97, 142, 142, 97, 1, 1, 1, 1, 9, 38, 97, 97, 131, 131, 131, 131, 131, 142, 142, 142, 142, 142, 97, 1, 1] 155 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 674 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.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003445 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CC3)C(C3CC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 124, 133, 133, 113, 28, 28, 6, 6, 6, 6, 6, 6, 16, 16, 1, 1, 1, 1, 6, 133, 133, 133, 133, 113, 28, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 6, 133, 133] 145 rigid atoms, others: [35, 36, 37, 38, 39, 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, 33, 34, 40, 41, 42]) total number of confs: 374 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003445 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003445 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003445/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003445 Building REAL300000003446 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003446' /scratch/stefan/7769584/working/building/REAL300000003446 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003446 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003446/0 /scratch/stefan/7769584/working/building/REAL300000003446 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/506 `/scratch/stefan/7769584/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003446 none C[NH+](C)CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 94, 78, 62, 78, 78, 32, 32, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 78, 78, 108, 108, 108, 108, 108, 108, 108, 108, 94, 94, 78, 78, 32, 6, 1, 1, 1, 1, 78, 78] 108 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 351 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003446 none C[NH+](C)CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 9, 9, 3, 1, 1, 1, 1, 1, 1, 11, 11, 47, 78, 78, 61, 78, 78, 78, 78, 78, 1, 1, 9, 9, 9, 9, 9, 9, 5, 5, 3, 3, 1, 1, 11, 47, 78, 78, 78, 78, 1, 1] 108 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 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, 41]) total number of confs: 269 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003446 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003446 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003446/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003446 Building REAL300000003447 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003447' /scratch/stefan/7769584/working/building/REAL300000003447 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003447 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003447/0 /scratch/stefan/7769584/working/building/REAL300000003447 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/507 `/scratch/stefan/7769584/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003447 none CCNC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 164, 103, 164, 103, 103, 103, 103, 32, 32, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 103, 201, 201, 201, 201, 201, 164, 103, 103, 103, 32, 6, 1, 1, 1, 1, 103] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003447 none CCNC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 66, 103, 103, 67, 102, 103, 103, 103, 103, 1, 17, 17, 17, 17, 17, 5, 1, 1, 1, 12, 66, 103, 103, 103, 103, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22, 38, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003447 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003447 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003447/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003447 Building REAL300000003448 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003448' /scratch/stefan/7769584/working/building/REAL300000003448 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003448 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003448/0 /scratch/stefan/7769584/working/building/REAL300000003448 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/508 `/scratch/stefan/7769584/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12) `REAL300000003448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003448 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 15, 15, 1, 1, 1, 1, 41, 41, 41] 41 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003448 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 41, 41, 41, 41, 1, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 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/7769584/working/building/REAL300000003448 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003448/1 /scratch/stefan/7769584/working/building/REAL300000003448 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/509 `/scratch/stefan/7769584/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12) `REAL300000003448.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003448 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 26, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 43, 44, 44, 44, 44, 44, 44, 44, 25, 6, 1, 1, 1, 1, 44, 44, 44] 44 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003448 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)OC2=CC=C(F)C=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 36, 44, 44, 37, 37, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 36, 44, 44, 44, 44, 1, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003448 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003448 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003448/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003448/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003448 Building REAL300000003449 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003449' /scratch/stefan/7769584/working/building/REAL300000003449 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003449 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003449/0 /scratch/stefan/7769584/working/building/REAL300000003449 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/510 `/scratch/stefan/7769584/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(Cl)C=C1F)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003449 none CC(CC1=CC=C(Cl)C=C1F)N=NC1=CC=C(C(=O)[O-])C=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', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 24, 42, 64, 64, 60, 64, 64, 64, 64, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 24, 24, 42, 42, 64, 64, 64, 1, 1, 1, 1] 64 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003449 none CC(CC1=CC=C(Cl)C=C1F)N=NC1=CC=C(C(=O)[O-])C=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', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 61, 61, 64, 64, 61, 61, 64, 64, 64, 64, 19, 19, 19, 19, 9, 9, 1, 1, 1, 64, 64, 64, 64] 64 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003449 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003449 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003449/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003449 Building REAL300000003450 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003450' /scratch/stefan/7769584/working/building/REAL300000003450 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003450 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003450/0 /scratch/stefan/7769584/working/building/REAL300000003450 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/511 `/scratch/stefan/7769584/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003450 none CN1N=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 81, 81, 81, 91, 91, 81, 91, 91, 81, 42, 42, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 90, 91, 84, 91, 91, 81, 42, 6, 1, 1, 1, 1] 91 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 179 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003450 none CN1N=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 34, 34, 77, 91, 91, 77, 91, 91, 91, 91, 91, 7, 7, 7, 1, 1, 1, 1, 1, 7, 33, 77, 91, 91, 91, 91] 91 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 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, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000003450 none CN1N=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 10, 10, 48, 80, 80, 48, 60, 80, 80, 80, 80, 2, 2, 2, 7, 6, 1, 6, 7, 1, 10, 48, 80, 80, 80, 80] 91 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 32] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003450 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003450 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003450/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003450 Building REAL300000003451 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003451' /scratch/stefan/7769584/working/building/REAL300000003451 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003451 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003451/0 /scratch/stefan/7769584/working/building/REAL300000003451 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/512 `/scratch/stefan/7769584/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C2=C1NC(=O)C2=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003451 none COC1=CC=C(Br)C2=C1NC(=O)C2=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 21, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 21, 7, 1, 1, 1, 1] 22 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003451 none COC1=CC=C(Br)C2=C1NC(=O)C2=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 21, 21, 22, 22, 22, 22, 3, 3, 3, 1, 1, 1, 7, 22, 22, 22, 22] 22 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 32, 34, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003451 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003451 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003451/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003451 Building REAL300000003452 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003452' /scratch/stefan/7769584/working/building/REAL300000003452 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003452 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003452/0 /scratch/stefan/7769584/working/building/REAL300000003452 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/513 `/scratch/stefan/7769584/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=CC=C3S2)C=C1) `REAL300000003452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003452 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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, 35, 39, 33, 39, 39, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 33, 11, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000003452 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 28, 39, 39, 39, 39, 39, 39, 39, 38, 39, 1, 1, 1, 1, 8, 27, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003452 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003452 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003452/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003452 Building REAL300000003453 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003453' /scratch/stefan/7769584/working/building/REAL300000003453 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003453 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003453/0 /scratch/stefan/7769584/working/building/REAL300000003453 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/514 `/scratch/stefan/7769584/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C([O-])=C1F) `REAL300000003453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003453 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C([O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 21, 27, 27, 21, 21, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003453 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C([O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 20, 6, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003453 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003453/1 /scratch/stefan/7769584/working/building/REAL300000003453 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/515 `/scratch/stefan/7769584/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1F) `REAL300000003453.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003453 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 32, 39, 39, 32, 32, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 32, 39, 39, 39, 39, 1, 1, 2] 78 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 144 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: REAL300000003453 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(F)C(O)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 5, 1, 1, 1, 1, 39, 39, 78] 78 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003453 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003453 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003453/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003453/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003453 Building REAL300000003454 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003454' /scratch/stefan/7769584/working/building/REAL300000003454 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003454 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003454/0 /scratch/stefan/7769584/working/building/REAL300000003454 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/516 `/scratch/stefan/7769584/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1N) `REAL300000003454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003454 none CC1=CC=C(Cl)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1N NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 17, 6, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 19, 20, 21, 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: REAL300000003454 none CC1=CC=C(Cl)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1N NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 25, 25, 22, 22, 25, 25, 25, 25, 1, 1, 2, 2, 2, 1, 1, 8, 22, 25, 25, 25, 25, 2, 2] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003454 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003454 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003454/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003454 Building REAL300000003455 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003455' /scratch/stefan/7769584/working/building/REAL300000003455 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003455 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003455/0 /scratch/stefan/7769584/working/building/REAL300000003455 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/517 `/scratch/stefan/7769584/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NNC2=CS(=O)(=O)C3=CC=CC=C23)C=C1) `REAL300000003455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003455 none O=C([O-])C1=CC=C(NNC2=CS(=O)(=O)C3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 4, 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 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, 30, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 30, 11, 1, 1, 1, 1, 1, 44, 44] 44 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 105 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003455 none O=C([O-])C1=CC=C(NNC2=CS(=O)(=O)C3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 4, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 20, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 10, 20, 44, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003455 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003455 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003455/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003455 Building REAL300000003456 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003456' /scratch/stefan/7769584/working/building/REAL300000003456 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003456 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003456/0 /scratch/stefan/7769584/working/building/REAL300000003456 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/518 `/scratch/stefan/7769584/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2Br)=N1) `REAL300000003456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003456 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2Br)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 35, 35, 130, 179, 179, 133, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 35, 130, 179, 179, 179, 179, 1, 1, 1, 1] 179 rigid atoms, others: [35, 36, 37, 38, 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]) total number of confs: 602 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003456 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2Br)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 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: [118, 118, 118, 49, 49, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 179, 179, 162, 179, 179, 179, 118, 118, 118, 118, 118, 49, 7, 1, 1, 1, 1, 179, 179, 179, 179] 179 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003456 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=CC=C2Br)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 12, 12, 74, 118, 118, 77, 102, 118, 118, 118, 118, 1, 1, 7, 7, 1, 7, 7, 7, 1, 2, 2, 2, 1, 12, 74, 118, 118, 118, 118, 7, 7, 2, 7] 179 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003456 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003456 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003456/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003456 Building REAL300000003457 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003457' /scratch/stefan/7769584/working/building/REAL300000003457 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003457 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003457/0 /scratch/stefan/7769584/working/building/REAL300000003457 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/519 `/scratch/stefan/7769584/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2C=CC=N2)C=C1) `REAL300000003457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003457 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2C=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 117, 117, 97, 117, 117, 97, 33, 33, 10, 10, 10, 9, 10, 10, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 97, 33, 10, 10, 10, 10, 1, 1, 1, 117, 117] 117 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 364 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003457 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2C=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [90, 86, 90, 66, 90, 90, 66, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 90, 90, 90, 90, 66, 10, 1, 1, 1, 1, 10, 10, 10, 90, 90] 117 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) 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: REAL300000003457 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2N2C=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003457 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003457 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003457/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003457 Building REAL300000003458 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003458' /scratch/stefan/7769584/working/building/REAL300000003458 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003458 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003458/0 /scratch/stefan/7769584/working/building/REAL300000003458 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/520 `/scratch/stefan/7769584/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NN(CC(F)(F)F)C=C2)C=C1) `REAL300000003458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003458 none O=C([O-])C1=CC=C(N=NCC2=NN(CC(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 69, 102, 63, 102, 102, 63, 63, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 102, 102, 102, 102, 9, 9, 9, 9, 1, 1, 102, 102] 201 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) 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: REAL300000003458 none O=C([O-])C1=CC=C(N=NCC2=NN(CC(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 40, 116, 116, 116, 201, 201, 201, 201, 116, 116, 1, 1, 1, 1, 40, 40, 201, 201, 116, 116, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003458 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003458/1 /scratch/stefan/7769584/working/building/REAL300000003458 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/521 `/scratch/stefan/7769584/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NN(CC(F)(F)F)C=C2)C=C1) `REAL300000003458.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003458 none O=C([O-])C1=CC=C(NN=CC2=NN(CC(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [40, 24, 40, 24, 40, 40, 24, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 40, 40, 40, 40, 24, 9, 9, 9, 1, 1, 40, 40] 77 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000003458 none O=C([O-])C1=CC=C(NN=CC2=NN(CC(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 1, 1, 11, 35, 36, 44, 44, 44, 77, 77, 77, 77, 44, 44, 1, 1, 1, 1, 11, 35, 77, 77, 44, 44, 1, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003458 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003458 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003458/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003458/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003458 Building REAL300000003459 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003459' /scratch/stefan/7769584/working/building/REAL300000003459 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003459 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003459/0 /scratch/stefan/7769584/working/building/REAL300000003459 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/522 `/scratch/stefan/7769584/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=CC([N+](=O)[O-])=CC=C23)C=C1) `REAL300000003459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003459 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC([N+](=O)[O-])=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 50, 57, 45, 57, 57, 45, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 57, 57, 57, 57, 45, 9, 1, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 17, 18, 22, 23, 24, 25, 26, 27]) 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: REAL300000003459 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC([N+](=O)[O-])=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 39, 39, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 11, 39, 58, 58, 56, 58, 58, 1, 1] 58 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003459 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003459 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003459/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003459 Building REAL300000003460 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003460' /scratch/stefan/7769584/working/building/REAL300000003460 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003460 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003460/0 /scratch/stefan/7769584/working/building/REAL300000003460 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/523 `/scratch/stefan/7769584/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC3=C2C2=C(C=CC=C2)N3)C=C1) `REAL300000003460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003460 none O=C([O-])C1=CC=C(NN=CC2=CC=CC3=C2C2=C(C=CC=C2)N3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 33, 48, 33, 48, 48, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48] 48 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 184 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: REAL300000003460 none O=C([O-])C1=CC=C(NN=CC2=CC=CC3=C2C2=C(C=CC=C2)N3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 12, 26, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003460 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003460 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003460/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003460 Building REAL300000003461 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003461' /scratch/stefan/7769584/working/building/REAL300000003461 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003461 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003461/0 /scratch/stefan/7769584/working/building/REAL300000003461 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/524 `/scratch/stefan/7769584/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(Br)=C2)C=C1) `REAL300000003461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003461 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 173, 201, 169, 201, 201, 169, 50, 50, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 169, 50, 11, 11, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 672 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003461 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 66, 105, 64, 105, 105, 64, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 3, 11, 11, 11, 105, 105, 105, 105, 64, 11, 1, 1, 11, 11, 9, 11, 105, 105] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003461 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 57, 57, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 12, 57, 121, 121, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003461 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003461 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003461/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003461 Building REAL300000003462 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003462' /scratch/stefan/7769584/working/building/REAL300000003462 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003462 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003462/0 /scratch/stefan/7769584/working/building/REAL300000003462 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/525 `/scratch/stefan/7769584/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(Cl)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003462 none COC1=NC(Cl)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 21, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 20, 6, 1, 1, 1, 1] 23 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003462 none COC1=NC(Cl)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 18, 23, 23, 18, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 6, 18, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003462 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003462 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003462/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003462 Building REAL300000003463 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003463' /scratch/stefan/7769584/working/building/REAL300000003463 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003463 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003463/0 /scratch/stefan/7769584/working/building/REAL300000003463 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/526 `/scratch/stefan/7769584/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=N1) `REAL300000003463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003463 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 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, 25, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 6, 1, 1, 1, 1] 32 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003463 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 28, 32, 32, 28, 32, 32, 32, 32, 32, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 9, 28, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 24, 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/7769584/working/building/REAL300000003463 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003463 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003463/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003463 Building REAL300000003464 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003464' /scratch/stefan/7769584/working/building/REAL300000003464 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003464 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003464/0 /scratch/stefan/7769584/working/building/REAL300000003464 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/527 `/scratch/stefan/7769584/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=NC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003464 none CC1=CC(Br)=NC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 22, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 21, 6, 1, 1, 1, 1] 39 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000003464 none CC1=CC(Br)=NC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 33, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 13, 33, 39, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003464 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003464 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003464/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003464 Building REAL300000003465 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003465' /scratch/stefan/7769584/working/building/REAL300000003465 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003465 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003465/0 /scratch/stefan/7769584/working/building/REAL300000003465 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/528 `/scratch/stefan/7769584/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)F)=C2F)C=C1) `REAL300000003465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003465 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [61, 44, 61, 43, 61, 61, 43, 11, 11, 1, 1, 1, 1, 1, 1, 1, 10, 10, 1, 1, 61, 61, 61, 61, 43, 11, 1, 1, 1, 10, 61, 61] 69 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 29, 30, 31]) 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: REAL300000003465 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 10, 33, 33, 61, 61, 42, 61, 61, 69, 69, 61, 61, 1, 1, 1, 1, 10, 33, 61, 61, 61, 69, 1, 1] 69 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003465 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003465 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003465/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003465 Building REAL300000003466 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003466' /scratch/stefan/7769584/working/building/REAL300000003466 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003466 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003466/0 /scratch/stefan/7769584/working/building/REAL300000003466 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/529 `/scratch/stefan/7769584/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(N2C=CC(C(F)(F)F)=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003466 none CC1=CC(N2C=CC(C(F)(F)F)=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [55, 55, 55, 48, 55, 76, 76, 76, 76, 76, 76, 76, 76, 55, 55, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 76, 76, 55, 55, 28, 6, 1, 1, 1, 1] 76 rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003466 none CC1=CC(N2C=CC(C(F)(F)F)=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 1, 2, 24, 26, 64, 76, 76, 64, 64, 76, 76, 76, 76, 5, 5, 5, 5, 1, 1, 5, 5, 23, 64, 76, 76, 76, 76] 76 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 12] set([0, 1, 2, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000003466 none CC1=CC(N2C=CC(C(F)(F)F)=N2)=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 13, 13, 45, 55, 55, 45, 45, 55, 55, 55, 55, 2, 2, 2, 1, 5, 5, 1, 1, 13, 45, 55, 55, 55, 55] 76 rigid atoms, others: [0, 1, 2, 3, 4, 16, 13, 14, 15, 34, 35, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003466 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003466 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003466/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003466 Building REAL300000003467 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003467' /scratch/stefan/7769584/working/building/REAL300000003467 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003467 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003467/0 /scratch/stefan/7769584/working/building/REAL300000003467 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/530 `/scratch/stefan/7769584/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003467 none CCOC1=CC=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 109, 80, 80, 80, 40, 80, 80, 80, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 80, 80, 80, 39, 6, 1, 1, 1, 1] 119 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003467 none CCOC1=CC=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 43, 80, 80, 43, 43, 80, 80, 80, 80, 36, 36, 36, 36, 36, 1, 1, 1, 12, 43, 80, 80, 80, 80] 119 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003467 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003467 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003467/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003467 Building REAL300000003468 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003468' /scratch/stefan/7769584/working/building/REAL300000003468 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003468 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003468/0 /scratch/stefan/7769584/working/building/REAL300000003468 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/531 `/scratch/stefan/7769584/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCN(CC(F)(F)F)C2)C=C1) `REAL300000003468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003468 none O=C([O-])C1=CC=C(N=NC2CCCN(CC(F)(F)F)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 7, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 10, 10] 18 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 14, 19, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 17, 18, 35, 20, 21, 22, 23, 36, 31]) 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: REAL300000003468 none O=C([O-])C1=CC=C(N=NC2CCCN(CC(F)(F)F)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 18, 18, 18, 18, 12, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 18, 18, 12, 12, 1, 1] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 20, 21, 22, 23, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003468 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003468 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003468/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003468 Building REAL300000003469 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003469' /scratch/stefan/7769584/working/building/REAL300000003469 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003469 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003469/0 /scratch/stefan/7769584/working/building/REAL300000003469 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/532 `/scratch/stefan/7769584/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)C=C2)C=C1) `REAL300000003469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003469 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 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, 87, 98, 98, 87, 25, 25, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 87, 25, 6, 6, 1, 1, 1, 1, 98, 98] 98 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 282 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003469 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [93, 77, 93, 64, 93, 93, 62, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 2, 6, 6, 93, 93, 93, 93, 62, 11, 1, 1, 6, 6, 6, 6, 93, 93] 98 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003469 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 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, 1, 1, 12, 47, 47, 93, 93, 93, 93, 93, 98, 98, 98, 98, 98, 98, 1, 1, 1, 1, 12, 47, 93, 93, 98, 98, 98, 98, 1, 1] 98 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003469 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003469 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003469/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003469 Building REAL300000003470 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003470' /scratch/stefan/7769584/working/building/REAL300000003470 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003470 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003470/0 /scratch/stefan/7769584/working/building/REAL300000003470 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/533 `/scratch/stefan/7769584/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1F) `REAL300000003470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003470 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 33, 41, 41, 33, 33, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 41, 41, 41, 41, 1, 1, 1] 41 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 148 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003470 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 2, 2, 7, 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: [28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 41, 41, 33, 40, 41, 41, 41, 29, 29, 29, 5, 1, 1, 1, 1, 41, 41, 41] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003470 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003470 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003470/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003470 Building REAL300000003471 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003471' /scratch/stefan/7769584/working/building/REAL300000003471 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003471 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003471/0 /scratch/stefan/7769584/working/building/REAL300000003471 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/534 `/scratch/stefan/7769584/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1C(C)CCCC1(C)C)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003471 none CC(CCC1C(C)CCCC1(C)C)N=NC1=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [22, 5, 22, 41, 44, 56, 56, 56, 54, 55, 55, 56, 56, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 22, 22, 42, 42, 44, 44, 56, 56, 56, 56, 56, 56, 56, 56, 54, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1] 56 rigid atoms, others: [51, 49, 50, 14, 15, 16, 17, 18, 19, 52, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 237 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: REAL300000003471 none CC(CCC1C(C)CCCC1(C)C)N=NC1=CC=C(C(=O)[O-])C=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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [20, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 55, 55, 56, 56, 55, 55, 56, 56, 56, 56, 20, 20, 20, 20, 6, 6, 4, 4, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 56, 56, 56, 56] 56 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 39, 12, 11, 40, 41, 38, 42, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003471 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003471 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003471/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003471 Building REAL300000003472 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003472' /scratch/stefan/7769584/working/building/REAL300000003472 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003472 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003472/0 /scratch/stefan/7769584/working/building/REAL300000003472 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/535 `/scratch/stefan/7769584/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=NN1C) `REAL300000003472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003472 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 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, 2, 2, 7, 7, 7, 7, 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: [10, 1, 10, 10, 36, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 10, 36, 38, 38, 38, 38, 1, 2, 2, 2] 38 rigid atoms, others: [1, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) 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: REAL300000003472 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 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, 2, 2, 7, 7, 7, 7, 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: [26, 26, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 26, 6, 1, 1, 1, 1, 38, 38, 38, 38] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003472 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003472 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003472/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003472 Building REAL300000003473 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003473' /scratch/stefan/7769584/working/building/REAL300000003473 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003473 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003473/0 /scratch/stefan/7769584/working/building/REAL300000003473 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/536 `/scratch/stefan/7769584/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NNC1=CC=C(C(=O)[O-])C=C1)=C1C=NC2=CC(C)=NN2C1=O) `REAL300000003473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003473 none CC(NNC1=CC=C(C(=O)[O-])C=C1)=C1C=NC2=CC(C)=NN2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 29, 38, 38, 29, 29, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 29, 38, 38, 38, 38, 1, 1, 2, 2, 2] 38 rigid atoms, others: [0, 1, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003473 none CC(NNC1=CC=C(C(=O)[O-])C=C1)=C1C=NC2=CC(C)=NN2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 7, 1, 1, 1, 1, 38, 38, 38, 38, 38] 38 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003473 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003473 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003473/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003473 Building REAL300000003474 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003474' /scratch/stefan/7769584/working/building/REAL300000003474 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003474 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003474/0 /scratch/stefan/7769584/working/building/REAL300000003474 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/537 `/scratch/stefan/7769584/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1) `REAL300000003474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003474 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.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, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 9, 43, 43, 105, 142, 142, 105, 108, 142, 142, 142, 142, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 43, 43, 43, 105, 142, 142, 142, 142, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1] 142 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 541 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003474 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.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, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 62, 116, 116, 62, 65, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 12, 62, 116, 116, 116, 116, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9] 142 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 550 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: REAL300000003474 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.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, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 116, 116, 116, 116, 116, 116, 142, 142, 142, 35, 35, 35, 6, 1, 1, 1, 1, 116, 116, 116, 116, 142, 142, 142, 142, 142, 142, 142] 142 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 265 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003474 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003474/1 /scratch/stefan/7769584/working/building/REAL300000003474 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/538 `/scratch/stefan/7769584/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1) `REAL300000003474.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003474 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 7, 30, 83, 83, 88, 88, 83, 83, 88, 88, 88, 88, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 30, 30, 30, 30, 88, 88, 88, 88, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1] 88 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 211 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003474 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 50, 50, 67, 67, 50, 50, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 10, 10, 10, 67, 67, 67, 67, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7] 88 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003474 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 67, 67, 67, 67, 67, 67, 88, 88, 88, 32, 32, 32, 32, 1, 1, 1, 1, 67, 67, 67, 67, 88, 88, 88, 88, 88, 88, 88] 88 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 235 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003474 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003474 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003474/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003474/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003474 Building REAL300000003475 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003475' /scratch/stefan/7769584/working/building/REAL300000003475 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003475 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003475/0 /scratch/stefan/7769584/working/building/REAL300000003475 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/539 `/scratch/stefan/7769584/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1) `REAL300000003475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003475 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 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, 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, 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: [29, 6, 29, 29, 96, 155, 155, 97, 155, 155, 155, 155, 155, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 96, 155, 155, 155, 155, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 155 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 545 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003475 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 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, 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, 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, 1, 9, 9, 53, 118, 118, 53, 90, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 53, 118, 118, 118, 118, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 155 rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 519 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003475 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 5, 5, 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, 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, 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: [34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 118, 118, 118, 118, 118, 118, 155, 155, 155, 155, 155, 35, 35, 35, 6, 1, 1, 1, 1, 118, 118, 118, 118, 155, 155, 155, 155, 155, 155, 155, 155, 155] 155 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 310 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003475 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003475/1 /scratch/stefan/7769584/working/building/REAL300000003475 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/540 `/scratch/stefan/7769584/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1) `REAL300000003475.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003475 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 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, 7] dock color type numbers: [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, 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: [22, 7, 22, 60, 60, 63, 63, 63, 63, 63, 63, 63, 63, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 63, 63, 63, 63, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003475 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 41, 41, 47, 47, 45, 46, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 47, 47, 47, 47, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 63 rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 111 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: REAL300000003475 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN(C)N=C1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 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, 7] dock color type numbers: [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, 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: [21, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 47, 47, 47, 47, 47, 47, 63, 63, 63, 63, 63, 21, 21, 21, 21, 1, 1, 1, 1, 47, 47, 47, 47, 63, 63, 63, 63, 63, 63, 63, 63, 63] 63 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 167 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003475 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003475 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003475/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003475/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003475 Building REAL300000003476 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003476' /scratch/stefan/7769584/working/building/REAL300000003476 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003476 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003476/0 /scratch/stefan/7769584/working/building/REAL300000003476 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/541 `/scratch/stefan/7769584/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(NC(=O)C(C)(C)C)C=N1) `REAL300000003476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003476 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(NC(=O)C(C)(C)C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 51, 51, 74, 74, 51, 51, 74, 74, 74, 74, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 1, 1, 12, 12, 12, 12, 74, 74, 74, 74, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 86 rigid atoms, others: [1, 34, 45, 13, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003476 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(NC(=O)C(C)(C)C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 74, 74, 74, 74, 86, 86, 86, 86, 86, 86, 74, 74, 36, 36, 36, 36, 1, 1, 1, 1, 74, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 74] 86 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003476 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003476 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003476/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003476 Building REAL300000003477 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003477' /scratch/stefan/7769584/working/building/REAL300000003477 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003477 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003477/0 /scratch/stefan/7769584/working/building/REAL300000003477 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/542 `/scratch/stefan/7769584/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O) `REAL300000003477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003477 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 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] 1 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: [70, 70, 47, 70, 47, 47, 29, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 70, 70, 70, 47, 28, 6, 1, 1, 1, 1, 47, 94] 140 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003477 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Cl)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 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] 1 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: [11, 11, 1, 11, 1, 1, 1, 1, 9, 9, 35, 47, 47, 35, 35, 47, 47, 47, 47, 1, 1, 1, 1, 1, 12, 12, 12, 1, 9, 35, 47, 47, 47, 47, 1, 2] 140 rigid atoms, others: [2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 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/7769584/working/building/REAL300000003477 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003477 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003477/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003477 Building REAL300000003478 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003478' /scratch/stefan/7769584/working/building/REAL300000003478 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003478 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003478/0 /scratch/stefan/7769584/working/building/REAL300000003478 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/543 `/scratch/stefan/7769584/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NC3=C(COCC3)S2)C=C1) `REAL300000003478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003478 none O=C([O-])C1=CC=C(N=NCC2=NC3=C(COCC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 45, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 19, 20, 21, 22, 23, 24, 31]) 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: REAL300000003478 none O=C([O-])C1=CC=C(N=NCC2=NC3=C(COCC3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 13, 13, 45, 45, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003478 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003478 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003478/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003478 Building REAL300000003479 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003479' /scratch/stefan/7769584/working/building/REAL300000003479 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003479 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003479/0 /scratch/stefan/7769584/working/building/REAL300000003479 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/544 `/scratch/stefan/7769584/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1) `REAL300000003479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003479 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 201, 171, 201, 201, 171, 56, 56, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 171, 56, 11, 11, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 656 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003479 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 75, 115, 74, 115, 115, 74, 12, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 10, 11, 11, 11, 115, 115, 115, 115, 74, 12, 1, 1, 11, 11, 11, 11, 115, 115] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003479 none O=C([O-])C1=CC=C(NN=CC2=CNN=C2C2=CC=CC(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 50, 50, 114, 114, 114, 114, 114, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 50, 114, 114, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003479 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003479 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003479/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003479 Building REAL300000003480 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003480' /scratch/stefan/7769584/working/building/REAL300000003480 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003480 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003480/0 /scratch/stefan/7769584/working/building/REAL300000003480 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/545 `/scratch/stefan/7769584/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC=C2Br)C=C1) `REAL300000003480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003480 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 14, 18, 18, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 14, 6, 1, 1, 1, 18, 18] 18 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003480 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 18, 18, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 11, 18, 19, 19, 19, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003480 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003480 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003480/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003480 Building REAL300000003481 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003481' /scratch/stefan/7769584/working/building/REAL300000003481 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003481 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003481/0 /scratch/stefan/7769584/working/building/REAL300000003481 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/546 `/scratch/stefan/7769584/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC=C2OC(F)F)C=C1) `REAL300000003481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003481 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [45, 27, 45, 27, 45, 45, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 45, 45, 45, 45, 27, 8, 1, 1, 1, 22, 45, 45] 55 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 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: REAL300000003481 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 113, 113, 113, 65, 113, 113, 113, 179, 189, 189, 1, 1, 1, 1, 10, 32, 113, 113, 113, 189, 1, 1] 189 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003481 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003481 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003481/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003481 Building REAL300000003482 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003482' /scratch/stefan/7769584/working/building/REAL300000003482 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003482 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003482/0 /scratch/stefan/7769584/working/building/REAL300000003482 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/547 `/scratch/stefan/7769584/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1) `REAL300000003482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003482 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 78, 78, 70, 25, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 78, 78, 78, 78, 70, 25, 1, 1, 1, 1, 1, 5, 78, 78] 78 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003482 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 61, 66, 49, 66, 66, 48, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 65, 66, 66, 66, 47, 7, 5, 5, 3, 5, 5, 1, 65, 65] 78 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: REAL300000003482 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)N(C3=CC=CC=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 10, 41, 41, 65, 65, 65, 65, 77, 77, 65, 77, 77, 65, 65, 1, 1, 1, 1, 10, 41, 77, 77, 77, 77, 77, 65, 1, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003482 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003482 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003482/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003482 Building REAL300000003483 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003483' /scratch/stefan/7769584/working/building/REAL300000003483 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003483 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003483/0 /scratch/stefan/7769584/working/building/REAL300000003483 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/548 `/scratch/stefan/7769584/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC([N+](=O)[O-])=C2)C=C1) `REAL300000003483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003483 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 35, 49, 49, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 35, 11, 1, 1, 1, 49, 49] 49 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003483 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 9, 34, 49, 49, 49, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003483 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003483 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003483/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003483 Building REAL300000003484 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003484' /scratch/stefan/7769584/working/building/REAL300000003484 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003484 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003484/0 /scratch/stefan/7769584/working/building/REAL300000003484 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/549 `/scratch/stefan/7769584/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3CCCCC3)N=C2)C=C1) `REAL300000003484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003484 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CCCCC3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 173, 173, 146, 57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 173, 173, 173, 173, 146, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 173, 173] 173 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, 41]) total number of confs: 420 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003484 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CCCCC3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 65, 89, 89, 53, 8, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 89, 89, 89, 89, 52, 8, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 89, 89] 173 rigid atoms, others: [39, 9, 10, 11, 12, 13, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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: REAL300000003484 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CCCCC3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 40, 40, 89, 89, 89, 173, 173, 173, 173, 173, 89, 89, 1, 1, 1, 1, 11, 40, 89, 173, 173, 173, 173, 173, 173, 173, 173, 173, 173, 173, 89, 1, 1] 173 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003484 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003484 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003484/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003484 Building REAL300000003485 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003485' /scratch/stefan/7769584/working/building/REAL300000003485 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003485 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003485/0 /scratch/stefan/7769584/working/building/REAL300000003485 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/550 `/scratch/stefan/7769584/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C=C(Br)C=C2F)C=C1) `REAL300000003485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003485 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 23, 20, 23, 23, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 20, 6, 1, 1, 24, 24] 24 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003485 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 19, 20, 24, 24, 24, 20, 24, 24, 24, 24, 1, 1, 1, 1, 11, 19, 24, 24, 1, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003485 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003485 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003485/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003485 Building REAL300000003486 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003486' /scratch/stefan/7769584/working/building/REAL300000003486 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003486 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003486/0 /scratch/stefan/7769584/working/building/REAL300000003486 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/551 `/scratch/stefan/7769584/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1) `REAL300000003486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003486 none CN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [133, 56, 133, 201, 201, 56, 56, 56, 22, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 133, 133, 133, 201, 201, 201, 201, 603, 56, 55, 21, 5, 1, 1, 1, 1, 56] 603 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 1263 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003486 none CN(CCO)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 34, 50, 1, 1, 1, 1, 1, 6, 6, 33, 55, 55, 33, 33, 55, 55, 55, 55, 1, 1, 10, 10, 10, 34, 34, 50, 50, 150, 1, 1, 6, 33, 55, 55, 55, 55, 1] 603 rigid atoms, others: [32, 1, 5, 6, 7, 8, 9, 39, 21, 22, 31] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 592 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003486 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003486 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003486/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003486 Building REAL300000003487 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003487' /scratch/stefan/7769584/working/building/REAL300000003487 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003487 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003487/0 /scratch/stefan/7769584/working/building/REAL300000003487 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/552 `/scratch/stefan/7769584/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1) `REAL300000003487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003487 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.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, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 3, 19, 59, 59, 60, 60, 59, 59, 60, 60, 60, 60, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 19, 60, 60, 60, 60, 1, 1, 1, 1, 1, 3, 3] 60 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 121 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003487 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.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, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 57, 57, 60, 60, 57, 57, 60, 60, 60, 60, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 12, 12, 12, 12, 60, 60, 60, 60, 3, 3, 1, 3, 3, 1, 1] 60 rigid atoms, others: [1, 37, 38, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 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: REAL300000003487 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.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, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 25, 25, 25, 25, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60] 60 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003487 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003487 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003487/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003487 Building REAL300000003488 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003488' /scratch/stefan/7769584/working/building/REAL300000003488 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003488 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003488/0 /scratch/stefan/7769584/working/building/REAL300000003488 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/553 `/scratch/stefan/7769584/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000003488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003488 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 23, 23, 25, 25, 23, 23, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 25, 25, 25, 25, 1, 1, 1, 1] 25 rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000003488 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 15, 15, 15, 1, 1, 1, 1, 25, 25, 25, 25] 25 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003488 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003488/1 /scratch/stefan/7769584/working/building/REAL300000003488 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/554 `/scratch/stefan/7769584/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000003488.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003488 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 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, 2, 2, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 14, 29, 29, 14, 14, 29, 29, 29, 29, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 29, 29, 29, 29, 1, 1, 1, 1] 29 rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003488 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 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, 2, 2, 7, 7, 7, 7, 7, 2, 2, 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: [26, 26, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 7, 1, 1, 1, 1, 29, 29, 29, 29] 29 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003488 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003488 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003488/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003488/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003488 Building REAL300000003489 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003489' /scratch/stefan/7769584/working/building/REAL300000003489 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003489 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003489/0 /scratch/stefan/7769584/working/building/REAL300000003489 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/555 `/scratch/stefan/7769584/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC=C1C(C)(C)C) `REAL300000003489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003489 none COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 10, 10, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 4, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 32 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003489 none COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 15 rigid atoms, others: [1, 2, 3, 4, 35, 33, 34, 16, 17, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 44 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003489 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003489 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003489/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003489 Building REAL300000003490 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003490' /scratch/stefan/7769584/working/building/REAL300000003490 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003490 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003490/0 /scratch/stefan/7769584/working/building/REAL300000003490 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/556 `/scratch/stefan/7769584/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Br)N=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003490 none CN1C=C(Br)N=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 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, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 17, 17, 1, 1, 1, 1] 40 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24]) 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: REAL300000003490 none CN1C=C(Br)N=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 17, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 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, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 2, 1, 9, 9, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003490 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003490 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003490/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003490 Building REAL300000003491 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003491' /scratch/stefan/7769584/working/building/REAL300000003491 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003491 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003491/0 /scratch/stefan/7769584/working/building/REAL300000003491 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/557 `/scratch/stefan/7769584/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1O) `REAL300000003491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003491 none COC1=CC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1O 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 75, 75, 30, 30, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 30, 7, 1, 1, 1, 1, 75, 150] 150 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003491 none COC1=CC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1O 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 53, 75, 75, 53, 62, 75, 75, 75, 75, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 9, 53, 75, 75, 75, 75, 1, 2] 150 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 25, 35] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003491 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003491 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003491/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003491 Building REAL300000003492 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003492' /scratch/stefan/7769584/working/building/REAL300000003492 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003492 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003492/0 /scratch/stefan/7769584/working/building/REAL300000003492 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/558 `/scratch/stefan/7769584/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC=C(F)C=C3NC2=O)C=C1) `REAL300000003492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003492 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=C(F)C=C3NC2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 10, 16, 16, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 10, 4, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 22, 23, 24, 25, 26, 27]) 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: REAL300000003492 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=C(F)C=C3NC2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 8, 15, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003492 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003492 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003492/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003492 Building REAL300000003493 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003493' /scratch/stefan/7769584/working/building/REAL300000003493 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003493 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003493/0 /scratch/stefan/7769584/working/building/REAL300000003493 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/559 `/scratch/stefan/7769584/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21) `REAL300000003493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003493 none CN1C(=O)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 18, 18, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 6, 1, 1, 1, 1, 20, 20, 20, 20, 20] 20 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 38 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003493 none CN1C(=O)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 14, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 14, 20, 20, 20, 20, 1, 1, 1, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 33, 34, 17, 18, 19, 20, 21, 22, 23, 36, 37] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003493 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003493 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003493/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003493 Building REAL300000003494 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003494' /scratch/stefan/7769584/working/building/REAL300000003494 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003494 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003494/0 /scratch/stefan/7769584/working/building/REAL300000003494 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/560 `/scratch/stefan/7769584/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1F) `REAL300000003494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003494 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 84, 164, 84, 84, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 164, 164, 164, 84, 37, 6, 1, 1, 1, 1, 84, 84] 164 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003494 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 15, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 1, 12, 1, 1, 1, 1, 10, 10, 59, 84, 84, 59, 59, 84, 84, 84, 84, 1, 1, 1, 1, 13, 13, 13, 1, 10, 59, 84, 84, 84, 84, 1, 1] 164 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003494 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003494 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003494/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003494 Building REAL300000003495 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003495' /scratch/stefan/7769584/working/building/REAL300000003495 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003495 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003495/0 /scratch/stefan/7769584/working/building/REAL300000003495 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/561 `/scratch/stefan/7769584/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003495 none O=C([O-])CCC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 60, 47, 47, 47, 47, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 47, 62, 62, 60, 60, 47, 47, 18, 18, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003495 none O=C([O-])CCC1=CC=C(CN=NC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [11, 9, 11, 6, 1, 1, 1, 1, 1, 1, 5, 37, 37, 47, 47, 37, 38, 47, 47, 47, 47, 1, 9, 9, 6, 6, 1, 1, 5, 5, 47, 47, 47, 47] 62 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003495 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003495/1 /scratch/stefan/7769584/working/building/REAL300000003495 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/562 `/scratch/stefan/7769584/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003495.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003495 none O=C([O-])CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 88, 83, 49, 49, 49, 49, 31, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 90, 90, 83, 83, 49, 49, 30, 6, 1, 1, 1, 1] 90 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003495 none O=C([O-])CCC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 18, 9, 1, 1, 1, 1, 1, 1, 6, 6, 21, 48, 48, 21, 21, 48, 48, 48, 48, 1, 17, 17, 9, 9, 1, 1, 6, 21, 49, 49, 48, 49] 90 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003495 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003495 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003495/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003495/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003495 Building REAL300000003496 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003496' /scratch/stefan/7769584/working/building/REAL300000003496 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003496 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003496/0 /scratch/stefan/7769584/working/building/REAL300000003496 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/563 `/scratch/stefan/7769584/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1O) `REAL300000003496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003496 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 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] 1 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: [78, 78, 51, 78, 51, 51, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 78, 78, 78, 51, 28, 6, 1, 1, 1, 1, 51, 102] 156 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003496 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 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] 1 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: [11, 11, 1, 11, 1, 1, 1, 1, 9, 9, 39, 51, 51, 39, 40, 51, 51, 51, 51, 1, 1, 1, 1, 1, 12, 12, 12, 1, 9, 39, 51, 51, 51, 51, 1, 2] 156 rigid atoms, others: [2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003496 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003496 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003496/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003496 Building REAL300000003497 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003497' /scratch/stefan/7769584/working/building/REAL300000003497 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003497 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003497/0 /scratch/stefan/7769584/working/building/REAL300000003497 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/564 `/scratch/stefan/7769584/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21) `REAL300000003497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003497 none CC1(C)CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 15 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: REAL300000003497 none CC1(C)CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44] set([35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29]) total number of confs: 19 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003497 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003497 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003497/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003497 Building REAL300000003498 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003498' /scratch/stefan/7769584/working/building/REAL300000003498 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003498 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003498/0 /scratch/stefan/7769584/working/building/REAL300000003498 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/565 `/scratch/stefan/7769584/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Br) `REAL300000003498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003498 none CC1=CC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Br NO_LONG_NAME dock atom types: ['C.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 45, 45, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 6, 1, 1, 1, 1, 45, 45, 45] 45 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003498 none CC1=CC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Br NO_LONG_NAME dock atom types: ['C.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 45, 45, 44, 45, 45, 45, 45, 45, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 39, 45, 45, 45, 45, 2, 2, 2] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003498 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003498 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003498/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003498 Building REAL300000003499 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003499' /scratch/stefan/7769584/working/building/REAL300000003499 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003499 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003499/0 /scratch/stefan/7769584/working/building/REAL300000003499 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/566 `/scratch/stefan/7769584/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1Br) `REAL300000003499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003499 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 21, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 43, 43, 43, 43, 1, 1, 1] 43 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 89 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003499 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(F)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 43, 43, 43, 43, 43, 43, 43, 26, 26, 26, 6, 1, 1, 1, 1, 43, 43, 43] 43 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 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/7769584/working/building/REAL300000003499 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003499 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003499/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003499 Building REAL300000003500 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003500' /scratch/stefan/7769584/working/building/REAL300000003500 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003500 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003500/0 /scratch/stefan/7769584/working/building/REAL300000003500 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/567 `/scratch/stefan/7769584/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1) `REAL300000003500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003500 none O=C([O-])C1=CC=C(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 35, 28, 35, 35, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 35, 35, 35, 35, 28, 7, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 16, 17, 22, 23, 24, 25, 26, 27]) 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: REAL300000003500 none O=C([O-])C1=CC=C(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 32, 32, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 7, 32, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003500 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003500/1 /scratch/stefan/7769584/working/building/REAL300000003500 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/568 `/scratch/stefan/7769584/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1) `REAL300000003500.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003500 none O=C([O-])C1=CC=C(N=NCC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 61, 63, 61, 63, 63, 61, 61, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 63, 63, 63, 63, 9, 9, 1, 1, 1, 1, 1, 63, 63] 63 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 16, 17, 22, 23, 24, 25, 26, 27]) 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: REAL300000003500 none O=C([O-])C1=CC=C(N=NCC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 18, 18, 63, 63, 63, 63, 63, 1, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003500 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003500 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003500/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003500/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003500 Building REAL300000003501 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003501' /scratch/stefan/7769584/working/building/REAL300000003501 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003501 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003501/0 /scratch/stefan/7769584/working/building/REAL300000003501 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/569 `/scratch/stefan/7769584/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC=CCC2=CC=C3OCOC3=C2)C=C1) `REAL300000003501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003501 none O=C([O-])C1=CC=C(N=NC=CCC2=CC=C3OCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 83, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 31, 31, 7, 7, 1, 1, 1, 1, 1, 83, 83] 83 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000003501 none O=C([O-])C1=CC=C(N=NC=CCC2=CC=C3OCOC3=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 22, 22, 48, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 22, 22, 48, 48, 83, 83, 83, 83, 83, 1, 1] 83 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003501 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003501 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003501/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003501 Building REAL300000003502 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003502' /scratch/stefan/7769584/working/building/REAL300000003502 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003502 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003502/0 /scratch/stefan/7769584/working/building/REAL300000003502 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/570 `/scratch/stefan/7769584/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CCC3)C=C2)C=C1) `REAL300000003502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003502 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 101, 107, 107, 94, 39, 39, 14, 9, 14, 14, 5, 1, 1, 1, 1, 1, 14, 14, 107, 107, 107, 107, 94, 39, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 107, 107] 107 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41]) total number of confs: 332 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003502 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 44, 46, 29, 46, 46, 25, 5, 5, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 1, 1, 46, 46, 46, 46, 25, 5, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 1, 1, 46, 46] 107 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) 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: REAL300000003502 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3CCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 33, 33, 46, 46, 37, 44, 83, 108, 108, 108, 46, 46, 1, 1, 1, 1, 9, 33, 46, 46, 83, 83, 108, 108, 108, 108, 108, 108, 108, 46, 46, 1, 1] 108 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003502 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003502 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003502/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003502 Building REAL300000003503 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003503' /scratch/stefan/7769584/working/building/REAL300000003503 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003503 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003503/0 /scratch/stefan/7769584/working/building/REAL300000003503 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/571 `/scratch/stefan/7769584/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)(F)C(F)(F)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003503 none COC(F)(F)C(F)(F)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 15, 5, 15, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 106, 184, 184, 36, 106, 106, 36, 85, 85, 36, 36, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 85, 85, 184, 184, 184, 85, 85, 36, 7, 1, 1, 1, 1, 85, 85] 184 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 878 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003503 none COC(F)(F)C(F)(F)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 15, 5, 15, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [55, 23, 5, 23, 23, 1, 5, 5, 1, 1, 1, 1, 1, 7, 7, 52, 85, 85, 60, 85, 85, 85, 85, 85, 1, 1, 55, 55, 55, 1, 1, 7, 52, 85, 85, 85, 85, 1, 1] 184 rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003503 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003503 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003503/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003503 Building REAL300000003504 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003504' /scratch/stefan/7769584/working/building/REAL300000003504 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003504 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003504/0 /scratch/stefan/7769584/working/building/REAL300000003504 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/572 `/scratch/stefan/7769584/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003504 none COC1=CC=C(CC(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 59, 59, 94, 94, 59, 28, 5, 28, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 94, 94, 94, 95, 95, 95, 94, 94, 59, 59, 28, 28, 28, 28, 1, 1, 1, 1, 94, 94, 94, 94] 95 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003504 none COC1=CC=C(CC(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 1, 1, 1, 1, 1, 7, 14, 14, 78, 78, 94, 94, 78, 78, 94, 94, 94, 94, 1, 1, 1, 3, 3, 3, 1, 1, 7, 7, 14, 14, 14, 14, 94, 94, 94, 94, 2, 2, 2, 1] 95 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003504 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003504 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003504/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003504 Building REAL300000003505 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003505' /scratch/stefan/7769584/working/building/REAL300000003505 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003505 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003505/0 /scratch/stefan/7769584/working/building/REAL300000003505 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/573 `/scratch/stefan/7769584/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=C(F)C=CC(F)=C1F)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003505 none CC(CC1=C(F)C=CC(F)=C1F)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 15, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [23, 4, 23, 44, 74, 74, 74, 74, 74, 74, 74, 74, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 44, 44, 74, 74, 1, 1, 1, 1] 74 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003505 none CC(CC1=C(F)C=CC(F)=C1F)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 15, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 73, 73, 74, 74, 73, 73, 74, 74, 74, 74, 19, 19, 19, 19, 7, 7, 1, 1, 74, 74, 74, 74] 74 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003505 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003505 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003505/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003505 Building REAL300000003506 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003506' /scratch/stefan/7769584/working/building/REAL300000003506 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003506 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003506/0 /scratch/stefan/7769584/working/building/REAL300000003506 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/574 `/scratch/stefan/7769584/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=C(F)C=CC(Cl)=C1F)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003506 none CC(CC1=C(F)C=CC(Cl)=C1F)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 15, 1, 1, 1, 16, 1, 15, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [23, 4, 23, 45, 77, 77, 77, 77, 77, 77, 77, 77, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 45, 45, 77, 77, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003506 none CC(CC1=C(F)C=CC(Cl)=C1F)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 15, 1, 1, 1, 16, 1, 15, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 75, 75, 77, 77, 75, 75, 77, 77, 77, 77, 20, 20, 20, 20, 7, 7, 1, 1, 77, 77, 77, 77] 77 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003506 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003506 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003506/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003506 Building REAL300000003507 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003507' /scratch/stefan/7769584/working/building/REAL300000003507 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003507 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003507/0 /scratch/stefan/7769584/working/building/REAL300000003507 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/575 `/scratch/stefan/7769584/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(Cl)=C2F)C=C1) `REAL300000003507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003507 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 47, 47, 47, 47, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 40, 10, 1, 1, 47, 48] 48 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 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: REAL300000003507 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 30, 30, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 10, 30, 48, 48, 1, 1] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003507 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003507 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003507/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003507 Building REAL300000003508 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003508' /scratch/stefan/7769584/working/building/REAL300000003508 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003508 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003508/0 /scratch/stefan/7769584/working/building/REAL300000003508 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/576 `/scratch/stefan/7769584/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1) `REAL300000003508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003508 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 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, 2, 2, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 17, 17, 17, 17, 1, 1, 1, 1, 1] 17 rigid atoms, others: [1, 34, 35, 36, 37, 38, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003508 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 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, 2, 2, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 17, 17, 17, 17, 17] 17 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 11, 12, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003508 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003508 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003508/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003508 Building REAL300000003509 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003509' /scratch/stefan/7769584/working/building/REAL300000003509 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003509 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003509/0 /scratch/stefan/7769584/working/building/REAL300000003509 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/577 `/scratch/stefan/7769584/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(C(F)(F)F)=C2)C=C1) `REAL300000003509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003509 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 104, 150, 150, 85, 12, 12, 1, 12, 50, 75, 75, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 150, 150, 150, 150, 85, 50, 50, 75, 75, 75, 75, 75, 1, 1, 1, 1, 150, 150] 201 rigid atoms, others: [36, 37, 38, 39, 9, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 760 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003509 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 108, 71, 108, 108, 66, 17, 17, 3, 1, 1, 1, 1, 17, 75, 75, 75, 75, 75, 75, 75, 75, 75, 108, 108, 108, 108, 66, 3, 3, 1, 1, 1, 1, 1, 75, 75, 75, 75, 108, 108] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 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, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41]) total number of confs: 454 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: REAL300000003509 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 35, 35, 96, 113, 113, 35, 158, 158, 158, 158, 158, 158, 158, 158, 158, 1, 1, 1, 1, 10, 96, 96, 113, 113, 113, 113, 113, 158, 158, 158, 158, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 528 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003509 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003509 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003509/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003509 Building REAL300000003510 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003510' /scratch/stefan/7769584/working/building/REAL300000003510 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003510 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003510/0 /scratch/stefan/7769584/working/building/REAL300000003510 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/578 `/scratch/stefan/7769584/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003510 none CC(C)(C)OC(=O)NC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 26, 36, 18, 18, 18, 18, 18, 14, 14, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 42, 42, 42, 42, 42, 42, 42, 42, 42, 26, 18, 18, 18, 14, 6, 1, 1, 1, 1, 18] 42 rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45]) 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: REAL300000003510 none CC(C)(C)OC(=O)NC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 15, 16, 16, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 18, 18, 12, 15, 18, 18, 18, 18, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 4, 12, 18, 18, 18, 18, 1] 42 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003510 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003510 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003510/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003510 Building REAL300000003511 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003511' /scratch/stefan/7769584/working/building/REAL300000003511 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003511 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003511/0 /scratch/stefan/7769584/working/building/REAL300000003511 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/579 `/scratch/stefan/7769584/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CC2(F)F)C=C1) `REAL300000003511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003511 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 189, 159, 58, 58, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 159, 58, 8, 8, 1, 1, 1, 189, 189] 189 rigid atoms, others: [14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003511 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [116, 116, 116, 105, 116, 116, 79, 12, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 116, 116, 116, 116, 79, 12, 1, 1, 8, 8, 8, 116, 116] 189 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003511 none O=C([O-])C1=CC=C(NN=CC2=CC=NN2C2CC2(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 33, 33, 64, 64, 64, 64, 64, 93, 93, 93, 93, 1, 1, 1, 1, 10, 33, 64, 64, 93, 93, 93, 1, 1] 93 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003511 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003511 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003511/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003511 Building REAL300000003512 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003512' /scratch/stefan/7769584/working/building/REAL300000003512 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003512 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003512/0 /scratch/stefan/7769584/working/building/REAL300000003512 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/580 `/scratch/stefan/7769584/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=CO1) `REAL300000003512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003512 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=CO1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 34, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 33, 6, 1, 1, 1, 1, 57] 57 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003512 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C(F)(F)F)=CO1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 46, 57, 57, 46, 47, 57, 57, 57, 57, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 9, 46, 57, 57, 57, 57, 1] 57 rigid atoms, others: [0, 1, 2, 3, 15, 16, 20, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003512 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003512 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003512/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003512 Building REAL300000003513 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003513' /scratch/stefan/7769584/working/building/REAL300000003513 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003513 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003513/0 /scratch/stefan/7769584/working/building/REAL300000003513 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/581 `/scratch/stefan/7769584/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=NC=CC=C12) `REAL300000003513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003513 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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] 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: [9, 1, 9, 9, 35, 53, 53, 35, 35, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 219 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003513 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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] dock color type numbers: [7, 7, 7, 4, 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] 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: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 53, 53, 53, 53, 53, 53, 53, 53, 53, 29, 29, 29, 6, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003513 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003513 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003513/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003513 Building REAL300000003514 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003514' /scratch/stefan/7769584/working/building/REAL300000003514 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003514 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003514/0 /scratch/stefan/7769584/working/building/REAL300000003514 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/582 `/scratch/stefan/7769584/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1C(F)F) `REAL300000003514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003514 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 35, 54, 54, 35, 35, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 35, 54, 54, 54, 54, 1, 1, 1, 1, 7] 54 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) 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: REAL300000003514 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 54, 54, 33, 54, 54, 54, 54, 54, 25, 25, 25, 5, 1, 1, 1, 1, 54, 54, 40, 54, 54] 54 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003514 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003514 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003514/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003514 Building REAL300000003515 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003515' /scratch/stefan/7769584/working/building/REAL300000003515 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003515 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003515/0 /scratch/stefan/7769584/working/building/REAL300000003515 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/583 `/scratch/stefan/7769584/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)N=C2)C=C1) `REAL300000003515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003515 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 133, 134, 134, 109, 56, 56, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 134, 134, 134, 134, 109, 56, 11, 11, 1, 1, 1, 11, 134, 134] 134 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003515 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 75, 91, 91, 56, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 91, 91, 91, 91, 56, 11, 1, 1, 11, 11, 11, 1, 91, 91] 134 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34]) 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: REAL300000003515 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 39, 39, 90, 90, 90, 90, 135, 135, 135, 135, 90, 90, 1, 1, 1, 1, 11, 39, 90, 90, 135, 135, 135, 90, 1, 1] 135 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003515 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003515 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003515/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003515 Building REAL300000003516 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003516' /scratch/stefan/7769584/working/building/REAL300000003516 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003516 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003516/0 /scratch/stefan/7769584/working/building/REAL300000003516 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/584 `/scratch/stefan/7769584/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1C1=CC=CC=C1) `REAL300000003516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003516 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1C1=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', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 4, 17, 17, 36, 57, 57, 36, 36, 57, 57, 57, 57, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 36, 57, 57, 57, 57, 4, 4, 4, 4, 1, 1, 1, 1, 1] 57 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 240 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003516 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1C1=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', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 30, 57, 57, 30, 30, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 9, 9, 9, 30, 57, 57, 57, 57, 1, 1, 1, 1, 4, 4, 1, 4, 4] 57 rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) 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: REAL300000003516 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC=C1C1=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', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 57, 57, 55, 57, 57, 57, 57, 57, 57, 57, 57, 27, 27, 27, 6, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 9, 10, 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: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003516 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003516 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003516/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003516 Building REAL300000003517 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003517' /scratch/stefan/7769584/working/building/REAL300000003517 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003517 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003517/0 /scratch/stefan/7769584/working/building/REAL300000003517 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/585 `/scratch/stefan/7769584/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C2O1) `REAL300000003517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003517 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', '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, 1, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 20, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 19, 5, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003517 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', '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, 1, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 25, 29, 29, 25, 26, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 9, 25, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/7769584/working/building/REAL300000003517 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003517 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003517/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003517 Building REAL300000003518 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003518' /scratch/stefan/7769584/working/building/REAL300000003518 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003518 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003518/0 /scratch/stefan/7769584/working/building/REAL300000003518 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/586 `/scratch/stefan/7769584/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCC(OCC3=CC=CC=C3)C2)C=C1) `REAL300000003518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003518 none O=C([O-])C1=CC=C(N=NC2CCC(OCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 117, 116, 116, 48, 48, 48, 48, 17, 3, 1, 1, 1, 1, 1, 1, 1, 48, 117, 117, 117, 117, 48, 48, 48, 48, 48, 48, 3, 3, 1, 1, 1, 1, 1, 48, 48, 117, 117] 117 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: 224 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003518 none O=C([O-])C1=CC=C(N=NC2CCC(OCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [34, 18, 34, 13, 34, 34, 13, 13, 1, 1, 1, 1, 1, 1, 8, 23, 48, 48, 28, 48, 48, 1, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 23, 23, 48, 48, 48, 48, 48, 1, 1, 34, 34] 117 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 21, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 335 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: REAL300000003518 none O=C([O-])C1=CC=C(N=NC2CCC(OCC3=CC=CC=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 42, 42, 42, 42, 81, 116, 116, 116, 116, 116, 116, 42, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 116, 116, 116, 116, 116, 116, 116, 42, 42, 1, 1] 116 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 325 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003518 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003518 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003518/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003518 Building REAL300000003519 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003519' /scratch/stefan/7769584/working/building/REAL300000003519 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003519 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003519/0 /scratch/stefan/7769584/working/building/REAL300000003519 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/587 `/scratch/stefan/7769584/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=CN12) `REAL300000003519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003519 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 19, 6, 1, 1, 1, 1, 20, 20, 20] 20 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 20, 21, 22, 23, 24, 25, 26, 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: REAL300000003519 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 4, 14, 20, 20, 20, 20, 1, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003519 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003519 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003519/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003519 Building REAL300000003520 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003520' /scratch/stefan/7769584/working/building/REAL300000003520 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003520 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003520/0 /scratch/stefan/7769584/working/building/REAL300000003520 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/588 `/scratch/stefan/7769584/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1) `REAL300000003520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003520 none CN1C=C(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 123, 123, 123, 123, 123, 43, 43, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 182, 182, 182, 182, 182, 182, 123, 123, 43, 7, 1, 1, 1, 1, 182] 182 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 274 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003520 none CN1C=C(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 83, 123, 123, 83, 83, 123, 123, 123, 123, 13, 13, 13, 13, 13, 13, 1, 1, 13, 83, 123, 123, 123, 123, 13] 182 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 484 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003520 none CN1C=C(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 69, 69, 153, 182, 182, 153, 153, 182, 182, 182, 182, 1, 1, 2, 2, 2, 1, 13, 13, 69, 153, 182, 182, 182, 182, 1] 182 rigid atoms, others: [0, 1, 2, 3, 4, 35, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 630 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003520 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003520 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003520/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003520 Building REAL300000003521 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003521' /scratch/stefan/7769584/working/building/REAL300000003521 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003521 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003521/0 /scratch/stefan/7769584/working/building/REAL300000003521 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/589 `/scratch/stefan/7769584/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1CCC(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)CC1) `REAL300000003521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003521 none CCCC1CCC(C(C)N=NC2=CC=C(C(=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 87, 57, 57, 57, 55, 30, 5, 30, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 56, 57, 88, 89, 89, 89, 89, 89, 89, 57, 57, 57, 57, 57, 57, 30, 30, 30, 30, 1, 1, 1, 1, 57, 57, 57, 57] 89 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 375 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: REAL300000003521 none CCCC1CCC(C(C)N=NC2=CC=C(C(=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 7, 1, 1, 1, 1, 1, 1, 8, 8, 40, 40, 57, 57, 40, 40, 57, 57, 57, 57, 1, 1, 10, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 57, 57, 57, 57, 1, 1, 1, 1] 89 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 46, 45, 20, 21, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 248 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003521 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003521 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003521/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003521 Building REAL300000003522 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003522' /scratch/stefan/7769584/working/building/REAL300000003522 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003522 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003522/0 /scratch/stefan/7769584/working/building/REAL300000003522 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/590 `/scratch/stefan/7769584/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CCC(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)CC1) `REAL300000003522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003522 none CC(C)C1CCC(C(C)N=NC2=CC=C(C(=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 46, 60, 46, 46, 45, 24, 5, 24, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 46, 60, 60, 60, 60, 60, 60, 60, 46, 46, 46, 46, 46, 46, 24, 24, 24, 24, 1, 1, 1, 1, 46, 46, 46, 46] 60 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003522 none CC(C)C1CCC(C(C)N=NC2=CC=C(C(=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 8, 1, 1, 1, 1, 1, 8, 8, 35, 35, 46, 46, 35, 35, 46, 46, 46, 46, 1, 1, 9, 9, 9, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 46, 46, 46, 46, 1, 1, 1, 1] 60 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 7, 44, 45, 46, 43, 20, 21, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003522 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003522 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003522/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003522 Building REAL300000003523 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003523' /scratch/stefan/7769584/working/building/REAL300000003523 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003523 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003523/0 /scratch/stefan/7769584/working/building/REAL300000003523 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/591 `/scratch/stefan/7769584/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Cl)=C2)C=C1) `REAL300000003523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003523 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 106, 147, 86, 147, 147, 84, 12, 12, 1, 12, 56, 84, 84, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 84, 56, 56, 84, 84, 84, 84, 84, 1, 1, 1, 1, 147, 147] 201 rigid atoms, others: [33, 34, 35, 36, 9, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 904 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003523 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 118, 72, 118, 118, 70, 17, 17, 3, 1, 1, 1, 1, 17, 84, 84, 84, 84, 84, 84, 118, 118, 118, 118, 70, 3, 3, 1, 1, 1, 1, 1, 84, 84, 84, 84, 118, 118] 201 rigid atoms, others: [32, 10, 11, 12, 13, 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, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 589 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: REAL300000003523 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 31, 31, 90, 114, 114, 31, 146, 146, 146, 146, 146, 146, 1, 1, 1, 1, 9, 90, 90, 114, 114, 114, 114, 114, 146, 146, 146, 146, 1, 1] 192 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 536 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003523 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003523 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003523/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003523 Building REAL300000003524 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003524' /scratch/stefan/7769584/working/building/REAL300000003524 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003524 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003524/0 /scratch/stefan/7769584/working/building/REAL300000003524 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/592 `/scratch/stefan/7769584/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CCC(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003524 none COC1=CC=C(CCC(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 91, 201, 201, 91, 69, 25, 5, 25, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 91, 86, 75, 75, 25, 25, 25, 25, 1, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 949 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003524 none COC1=CC=C(CCC(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 9, 35, 35, 159, 159, 201, 201, 159, 159, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 1, 1, 6, 6, 9, 9, 35, 35, 35, 35, 201, 201, 201, 201, 2, 2, 2, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003524 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003524 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003524/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003524 Building REAL300000003525 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003525' /scratch/stefan/7769584/working/building/REAL300000003525 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003525 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003525/0 /scratch/stefan/7769584/working/building/REAL300000003525 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/593 `/scratch/stefan/7769584/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21) `REAL300000003525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003525 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003525 none CC1CCC(N=NC2=CC=C(C(=O)[O-])C=C2)CC2=CC=CC=C21 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41] set([32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003525 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003525 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003525/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003525 Building REAL300000003526 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003526' /scratch/stefan/7769584/working/building/REAL300000003526 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003526 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003526/0 /scratch/stefan/7769584/working/building/REAL300000003526 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/594 `/scratch/stefan/7769584/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Cl) `REAL300000003526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003526 none CCCN1N=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 126, 126, 126, 126, 126, 38, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 198, 198, 126, 126, 126, 38, 6, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003526 none CCCN1N=C(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Cl 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 86, 126, 126, 86, 103, 126, 126, 126, 126, 1, 1, 12, 12, 12, 11, 11, 5, 5, 2, 2, 2, 13, 86, 126, 126, 126, 126] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21] set([0, 1, 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: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003526 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003526 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003526/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003526 Building REAL300000003527 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003527' /scratch/stefan/7769584/working/building/REAL300000003527 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003527 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003527/0 /scratch/stefan/7769584/working/building/REAL300000003527 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/595 `/scratch/stefan/7769584/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C#N)C1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003527 none CC(C)(C#N)C1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 2, 2, 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, 70, 155, 155, 155, 70, 70, 70, 37, 37, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 70, 155, 155, 155, 155, 155, 155, 70, 37, 7, 1, 1, 1, 1] 155 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003527 none CC(C)(C#N)C1=NC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 2, 2, 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: [12, 1, 12, 12, 13, 1, 1, 1, 1, 1, 6, 6, 50, 70, 70, 50, 55, 70, 69, 70, 70, 1, 13, 13, 13, 13, 12, 13, 1, 6, 49, 70, 70, 70, 70] 155 rigid atoms, others: [1, 5, 6, 7, 8, 9, 21, 28] set([0, 2, 3, 4, 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: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003527 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003527 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003527/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003527 Building REAL300000003528 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003528' /scratch/stefan/7769584/working/building/REAL300000003528 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003528 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003528/0 /scratch/stefan/7769584/working/building/REAL300000003528 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/596 `/scratch/stefan/7769584/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003528 none COC1=CC=C(Br)C(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 72, 116, 116, 116, 116, 43, 43, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 43, 6, 1, 1, 1, 1] 116 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000003528 none COC1=CC=C(Br)C(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 13, 13, 89, 116, 116, 114, 116, 116, 116, 116, 116, 3, 3, 3, 1, 1, 13, 89, 116, 116, 116, 116] 116 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003528 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003528 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003528/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003528 Building REAL300000003529 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003529' /scratch/stefan/7769584/working/building/REAL300000003529 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003529 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003529/0 /scratch/stefan/7769584/working/building/REAL300000003529 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/597 `/scratch/stefan/7769584/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=C(SC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2)S1) `REAL300000003529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003529 none COC(=O)C1=CC2=C(SC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 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, 7, 4, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 63, 77, 63, 63, 63, 63, 63, 38, 38, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 63, 63, 77, 77, 77, 63, 38, 7, 1, 1, 1, 1, 63] 77 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003529 none COC(=O)C1=CC2=C(SC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 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, 7, 4, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 8, 8, 46, 63, 63, 55, 63, 63, 63, 63, 63, 1, 1, 11, 10, 10, 1, 8, 45, 63, 63, 63, 63, 1] 77 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 34, 22, 23, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003529 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003529 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003529/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003529 Building REAL300000003530 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003530' /scratch/stefan/7769584/working/building/REAL300000003530 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003530 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003530/0 /scratch/stefan/7769584/working/building/REAL300000003530 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/598 `/scratch/stefan/7769584/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003530 none COC(=O)C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 201, 166, 166, 166, 79, 42, 21, 21, 21, 21, 21, 21, 14, 14, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 166, 201, 201, 201, 166, 166, 79, 79, 21, 21, 21, 21, 14, 6, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 501 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003530 none COC(=O)C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 89, 123, 89, 89, 89, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 21, 21, 18, 20, 21, 21, 21, 21, 89, 123, 123, 123, 89, 89, 19, 19, 1, 1, 1, 1, 4, 18, 21, 21, 21, 21] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003530 none COC(=O)C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 48, 89, 89, 89, 89, 89, 89, 113, 113, 166, 166, 166, 166, 166, 166, 166, 166, 166, 1, 3, 3, 3, 1, 1, 8, 8, 89, 89, 89, 89, 113, 164, 166, 166, 166, 166] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 28] set([0, 1, 3, 9, 10, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003530 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003530 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003530/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003530 Building REAL300000003531 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003531' /scratch/stefan/7769584/working/building/REAL300000003531 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003531 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003531/0 /scratch/stefan/7769584/working/building/REAL300000003531 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/599 `/scratch/stefan/7769584/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC(CC2=CC=CC=C2)CC2CCCCC2)C=C1) `REAL300000003531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003531 none O=C([O-])C1=CC=C(N=NC(CC2=CC=CC=C2)CC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [65, 51, 65, 46, 65, 65, 46, 46, 13, 6, 13, 32, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 13, 32, 32, 39, 39, 39, 39, 39, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65] 96 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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, 49, 50]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003531 none O=C([O-])C1=CC=C(N=NC(CC2=CC=CC=C2)CC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [62, 53, 62, 47, 62, 62, 47, 47, 9, 3, 1, 1, 1, 1, 1, 1, 1, 8, 29, 39, 39, 39, 39, 39, 62, 62, 62, 62, 9, 3, 3, 1, 1, 1, 1, 1, 29, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 62, 62] 96 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003531 none O=C([O-])C1=CC=C(N=NC(CC2=CC=CC=C2)CC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 31, 64, 69, 69, 69, 69, 69, 31, 63, 73, 73, 73, 73, 73, 1, 1, 1, 1, 31, 64, 64, 69, 69, 69, 69, 69, 63, 63, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1] 96 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 50, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003531 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003531 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003531/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003531 Building REAL300000003532 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003532' /scratch/stefan/7769584/working/building/REAL300000003532 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003532 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003532/0 /scratch/stefan/7769584/working/building/REAL300000003532 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/600 `/scratch/stefan/7769584/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1) `REAL300000003532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003532 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 154, 71, 21, 21, 21, 21, 21, 21, 12, 12, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 201, 154, 154, 21, 21, 21, 21, 12, 4, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003532 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 21, 21, 12, 16, 21, 21, 21, 21, 90, 90, 90, 27, 27, 1, 1, 1, 1, 4, 12, 21, 21, 21, 21] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) 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: REAL300000003532 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 47, 90, 90, 90, 90, 90, 90, 116, 116, 179, 201, 201, 184, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 90, 90, 90, 90, 116, 179, 201, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003532 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003532 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003532/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003532 Building REAL300000003533 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003533' /scratch/stefan/7769584/working/building/REAL300000003533 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003533 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003533/0 /scratch/stefan/7769584/working/building/REAL300000003533 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/601 `/scratch/stefan/7769584/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=CC(Br)=C1) `REAL300000003533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003533 none CC1=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 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, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 6, 1, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003533 none CC1=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 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, 7, 7, 22, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 22, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 33, 34, 17, 18, 19, 20, 21, 22, 26] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 27, 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/7769584/working/building/REAL300000003533 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003533 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003533/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003533 Building REAL300000003534 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003534' /scratch/stefan/7769584/working/building/REAL300000003534 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003534 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003534/0 /scratch/stefan/7769584/working/building/REAL300000003534 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/602 `/scratch/stefan/7769584/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(N2)C(Br)=CS3)C=C1) `REAL300000003534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003534 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(N2)C(Br)=CS3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 14, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 24, 27, 27, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 24, 7, 1, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003534 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(N2)C(Br)=CS3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 14, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 24, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 8, 23, 27, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003534 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003534 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003534/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003534 Building REAL300000003535 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003535' /scratch/stefan/7769584/working/building/REAL300000003535 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003535 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003535/0 /scratch/stefan/7769584/working/building/REAL300000003535 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/603 `/scratch/stefan/7769584/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=C1) `REAL300000003535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003535 none N#CC1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', '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, 1, 11, 11, 1, 1, 1, 17, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [46, 47, 46, 47, 47, 47, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 27, 6, 1, 1, 1, 1, 47] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 29]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003535 none N#CC1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(Br)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', '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, 1, 11, 11, 1, 1, 1, 17, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 41, 47, 47, 41, 47, 47, 47, 47, 47, 1, 1, 1, 1, 10, 41, 47, 47, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003535 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003535 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003535/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003535 Building REAL300000003536 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003536' /scratch/stefan/7769584/working/building/REAL300000003536 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003536 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003536/0 /scratch/stefan/7769584/working/building/REAL300000003536 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/604 `/scratch/stefan/7769584/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)C=C2)C=C1) `REAL300000003536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003536 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 37, 46, 46, 37, 15, 15, 3, 2, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 46, 46, 46, 46, 37, 15, 5, 5, 1, 1, 1, 5, 5, 46, 46] 46 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 154 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003536 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 29, 32, 24, 32, 32, 23, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 32, 32, 32, 32, 23, 6, 1, 1, 5, 5, 5, 1, 1, 32, 32] 46 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35]) 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: REAL300000003536 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CSC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 11, 25, 25, 33, 33, 26, 26, 46, 46, 46, 46, 33, 33, 1, 1, 1, 1, 11, 25, 33, 33, 46, 46, 46, 33, 33, 1, 1] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003536 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003536 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003536/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003536 Building REAL300000003537 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003537' /scratch/stefan/7769584/working/building/REAL300000003537 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003537 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003537/0 /scratch/stefan/7769584/working/building/REAL300000003537 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/605 `/scratch/stefan/7769584/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003537 none CC(F)(F)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 99, 169, 169, 99, 60, 99, 99, 36, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99, 169, 169, 169, 66, 99, 99, 35, 6, 1, 1, 1, 1, 99] 169 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 606 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003537 none CC(F)(F)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 57, 99, 99, 57, 74, 99, 99, 99, 99, 1, 13, 13, 13, 1, 1, 1, 11, 57, 99, 99, 99, 99, 1] 169 rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003537 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003537 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003537/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003537 Building REAL300000003538 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003538' /scratch/stefan/7769584/working/building/REAL300000003538 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003538 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003538/0 /scratch/stefan/7769584/working/building/REAL300000003538 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/606 `/scratch/stefan/7769584/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(CCC(C)N=NC2=CC=C(C(=O)[O-])C=C2)=CC=C1O) `REAL300000003538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003538 none CCOC1=CC(CCC(C)N=NC2=CC=C(C(=O)[O-])C=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', '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, 5, 12, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 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, 200, 138, 138, 138, 83, 72, 26, 4, 26, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 201, 201, 201, 201, 201, 138, 83, 80, 78, 78, 26, 26, 26, 26, 1, 1, 1, 1, 138, 138, 276] 402 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45]) total number of confs: 842 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: REAL300000003538 none CCOC1=CC(CCC(C)N=NC2=CC=C(C(=O)[O-])C=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', '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, 5, 12, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 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: [33, 9, 1, 1, 1, 1, 1, 8, 9, 26, 26, 98, 98, 138, 138, 98, 99, 138, 138, 138, 138, 1, 1, 1, 1, 34, 34, 34, 33, 33, 1, 8, 8, 9, 9, 26, 26, 26, 26, 138, 138, 138, 138, 1, 1, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 43, 44, 21, 22, 23, 24, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 620 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003538 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003538 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003538/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003538 Building REAL300000003539 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003539' /scratch/stefan/7769584/working/building/REAL300000003539 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003539 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003539/0 /scratch/stefan/7769584/working/building/REAL300000003539 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/607 `/scratch/stefan/7769584/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC3=CC(Cl)=CC=C23)C=C1) `REAL300000003539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003539 none O=C([O-])C1=CC=C(NN=CC2=CC=CC3=CC(Cl)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 40, 50, 50, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 12, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 21, 22, 23, 24, 25, 26]) 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: REAL300000003539 none O=C([O-])C1=CC=C(NN=CC2=CC=CC3=CC(Cl)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003539 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003539 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003539/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003539 Building REAL300000003540 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003540' /scratch/stefan/7769584/working/building/REAL300000003540 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003540 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003540/0 /scratch/stefan/7769584/working/building/REAL300000003540 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/608 `/scratch/stefan/7769584/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003540 none COC(=O)CC1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 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, 130, 201, 61, 61, 61, 61, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 130, 130, 61, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003540 none COC(=O)CC1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 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: [31, 31, 5, 31, 1, 1, 1, 1, 1, 1, 9, 59, 59, 61, 61, 59, 59, 61, 61, 61, 61, 1, 31, 31, 31, 5, 5, 1, 9, 9, 61, 61, 61, 61] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003540 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003540 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003540/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003540 Building REAL300000003541 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003541' /scratch/stefan/7769584/working/building/REAL300000003541 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003541 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003541/0 /scratch/stefan/7769584/working/building/REAL300000003541 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/609 `/scratch/stefan/7769584/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003541 none CC1=CC=CN=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 194, 194, 194, 128, 128, 128, 128, 36, 5, 36, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 128, 194, 194, 194, 194, 194, 194, 128, 36, 36, 36, 36, 1, 1, 1, 1] 194 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 350 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003541 none CC1=CC=CN=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 91, 91, 128, 128, 91, 91, 128, 128, 128, 128, 1, 10, 10, 10, 10, 10, 10, 1, 13, 13, 13, 13, 128, 128, 128, 128] 194 rigid atoms, others: [6, 7, 8, 9, 10, 11, 24, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003541 none CC1=CC=CN=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 79, 79, 189, 189, 194, 194, 189, 189, 194, 194, 194, 194, 10, 2, 2, 2, 1, 1, 1, 10, 79, 79, 79, 79, 194, 194, 194, 194] 194 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]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003541 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003541/1 /scratch/stefan/7769584/working/building/REAL300000003541 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/610 `/scratch/stefan/7769584/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=C2C)S1) `REAL300000003541.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003541 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 5, 14, 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, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [68, 10, 66, 68, 123, 138, 138, 123, 138, 138, 138, 138, 138, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 68, 68, 68, 123, 138, 138, 138, 138, 10, 1, 1, 1, 2, 2, 2] 138 rigid atoms, others: [34, 35, 36, 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, 37, 38, 39]) total number of confs: 438 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003541 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 5, 14, 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, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 65, 106, 106, 65, 89, 105, 105, 106, 106, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 13, 13, 13, 64, 106, 106, 106, 106, 1, 10, 10, 10, 10, 10, 10] 138 rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 446 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003541 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 5, 14, 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, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 106, 106, 106, 106, 138, 138, 138, 138, 138, 138, 106, 36, 36, 36, 7, 1, 1, 1, 1, 106, 138, 138, 138, 138, 138, 138] 138 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 9, 10, 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: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003541 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003541 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003541/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003541/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003541 Building REAL300000003542 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003542' /scratch/stefan/7769584/working/building/REAL300000003542 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003542 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003542/0 /scratch/stefan/7769584/working/building/REAL300000003542 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/611 `/scratch/stefan/7769584/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C(C)=C(OC)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C) `REAL300000003542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003542 none COC1=C(C)C(C)=C(OC)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 5, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 118, 118, 117, 118, 118, 118, 118, 118, 139, 37, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 139, 139, 139, 118, 118, 118, 118, 118, 118, 139, 139, 139, 36, 6, 1, 1, 1, 1, 118, 118, 118] 139 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45]) total number of confs: 250 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003542 none COC1=C(C)C(C)=C(OC)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 5, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 9, 9, 71, 118, 118, 76, 71, 118, 118, 118, 118, 1, 1, 3, 3, 3, 2, 2, 2, 2, 2, 2, 4, 4, 4, 9, 71, 118, 118, 118, 118, 2, 2, 2] 139 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 23, 24] set([0, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 500 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003542 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003542 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003542/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003542 Building REAL300000003543 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003543' /scratch/stefan/7769584/working/building/REAL300000003543 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003543 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003543/0 /scratch/stefan/7769584/working/building/REAL300000003543 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/612 `/scratch/stefan/7769584/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(Br)=C2F)C=C1) `REAL300000003543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003543 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(Br)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 16, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 27, 27, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 24, 7, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003543 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(Br)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 16, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 23, 23, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 23, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003543 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003543 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003543/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003543 Building REAL300000003544 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003544' /scratch/stefan/7769584/working/building/REAL300000003544 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003544 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003544/0 /scratch/stefan/7769584/working/building/REAL300000003544 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/613 `/scratch/stefan/7769584/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2CCCCC2)C=C1) `REAL300000003544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003544 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 162, 190, 162, 190, 190, 162, 55, 55, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 162, 55, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 190, 190] 190 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45]) total number of confs: 588 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003544 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 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: [77, 41, 77, 41, 77, 77, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 23, 77, 77, 77, 77, 41, 10, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 77, 77] 190 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 395 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: REAL300000003544 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 35, 35, 78, 78, 78, 78, 78, 78, 148, 192, 192, 192, 192, 192, 1, 1, 1, 1, 9, 35, 78, 78, 78, 78, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 1, 1] 192 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 419 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003544 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003544 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003544/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003544 Building REAL300000003545 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003545' /scratch/stefan/7769584/working/building/REAL300000003545 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003545 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003545/0 /scratch/stefan/7769584/working/building/REAL300000003545 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/614 `/scratch/stefan/7769584/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)C=C1) `REAL300000003545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003545 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 181, 201, 201, 181, 69, 69, 9, 12, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 181, 69, 37, 37, 1, 1, 1, 1, 37, 37, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39]) total number of confs: 664 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003545 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 39, 22, 39, 39, 22, 4, 4, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 37, 37, 1, 1, 39, 39, 39, 39, 22, 4, 1, 1, 37, 37, 37, 37, 1, 1, 39, 39] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39]) 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: REAL300000003545 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 26, 26, 39, 39, 27, 27, 109, 201, 201, 201, 201, 201, 201, 39, 39, 1, 1, 1, 1, 8, 26, 39, 39, 201, 201, 201, 201, 39, 39, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003545 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003545 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003545/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003545 Building REAL300000003546 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003546' /scratch/stefan/7769584/working/building/REAL300000003546 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003546 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003546/0 /scratch/stefan/7769584/working/building/REAL300000003546 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/615 `/scratch/stefan/7769584/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2COC2CCCCC2)C=C1) `REAL300000003546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003546 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2COC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 121, 121, 57, 57, 57, 57, 57, 57, 11, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 121, 57, 57, 57, 57, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 47, 48]) total number of confs: 546 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003546 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2COC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 44, 54, 44, 54, 54, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 57, 57, 57, 57, 57, 54, 54, 54, 54, 44, 12, 1, 1, 1, 1, 7, 7, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 54, 54] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) 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: REAL300000003546 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2COC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 22, 22, 65, 65, 65, 65, 65, 65, 114, 185, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 22, 65, 65, 65, 65, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 48, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 532 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003546 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003546 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003546/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003546 Building REAL300000003547 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003547' /scratch/stefan/7769584/working/building/REAL300000003547 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003547 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003547/0 /scratch/stefan/7769584/working/building/REAL300000003547 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/616 `/scratch/stefan/7769584/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(Cl)C=C2)C=C1) `REAL300000003547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003547 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 194, 201, 201, 194, 110, 110, 73, 73, 73, 73, 73, 73, 21, 3, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 194, 110, 73, 73, 73, 73, 3, 3, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003547 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens 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, 22, 37, 22, 37, 37, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 73, 73, 73, 73, 73, 73, 37, 37, 37, 37, 22, 4, 1, 1, 1, 1, 35, 35, 73, 73, 73, 73, 37, 37] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000003547 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 17, 17, 37, 37, 19, 37, 37, 37, 81, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 4, 17, 37, 37, 37, 37, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003547 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003547 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003547/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003547 Building REAL300000003548 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003548' /scratch/stefan/7769584/working/building/REAL300000003548 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003548 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003548/0 /scratch/stefan/7769584/working/building/REAL300000003548 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/617 `/scratch/stefan/7769584/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1) `REAL300000003548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003548 none COC1=CC=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 97, 45, 30, 45, 45, 18, 18, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 201, 201, 201, 201, 201, 201, 201, 45, 45, 18, 6, 1, 1, 1, 1, 45, 45, 201] 201 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 392 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003548 none COC1=CC=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 45, 45, 29, 45, 45, 45, 45, 45, 1, 1, 19, 35, 35, 35, 19, 19, 19, 1, 1, 6, 29, 45, 45, 45, 45, 1, 1, 19] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 41, 24, 25, 42] 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, 35, 36, 37, 38, 39, 40, 43]) 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: REAL300000003548 none COC1=CC=CC(OC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 19, 19, 9, 19, 67, 67, 152, 201, 201, 155, 201, 201, 201, 201, 201, 19, 19, 1, 3, 3, 3, 1, 1, 1, 19, 19, 67, 152, 201, 201, 201, 201, 19, 19, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003548 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003548 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003548/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003548 Building REAL300000003549 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003549' /scratch/stefan/7769584/working/building/REAL300000003549 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003549 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003549/0 /scratch/stefan/7769584/working/building/REAL300000003549 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/618 `/scratch/stefan/7769584/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C21) `REAL300000003549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003549 none CCN1CCCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 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, 61, 61, 61, 61, 61, 61, 61, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 61, 61, 61, 74, 74, 74, 74, 74, 61, 61, 61, 61, 61, 61, 61, 33, 7, 1, 1, 1, 1, 61, 61] 74 rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 178 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: REAL300000003549 none CCN1CCCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 61, 61, 50, 59, 61, 61, 61, 61, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 48, 61, 61, 61, 61, 1, 1] 74 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 42, 7, 34, 43, 35, 21, 22, 23, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41]) total number of confs: 197 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003549 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003549/1 /scratch/stefan/7769584/working/building/REAL300000003549 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/619 `/scratch/stefan/7769584/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCC2=CC(C=[NH+]NC3=CC=C(C(=O)[O-])C=C3)=CC=C21) `REAL300000003549.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003549 none CCN1CCCC2=CC(C=[NH+]NC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 14, 7, 1, 1, 1, 1, 42, 42] 42 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 77 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: REAL300000003549 none CCN1CCCC2=CC(C=[NH+]NC3=CC=C(C(=O)[O-])C=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 32, 42, 42, 32, 32, 42, 42, 42, 42, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 32, 42, 42, 42, 42, 1, 1] 42 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 44, 34, 43, 35, 22, 23, 24, 36, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003549 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003549 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003549/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003549/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003549 Building REAL300000003550 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003550' /scratch/stefan/7769584/working/building/REAL300000003550 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003550 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003550/0 /scratch/stefan/7769584/working/building/REAL300000003550 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/620 `/scratch/stefan/7769584/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=CC=C3N2)C=C1) `REAL300000003550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003550 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=CC=C3N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 26, 21, 26, 26, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 21, 6, 1, 1, 1, 1, 1, 26, 26] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003550 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(Br)C=CC=C3N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 9, 25, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 25, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003550 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003550 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003550/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003550 Building REAL300000003551 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003551' /scratch/stefan/7769584/working/building/REAL300000003551 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003551 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003551/0 /scratch/stefan/7769584/working/building/REAL300000003551 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/621 `/scratch/stefan/7769584/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000003551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003551 none CC1=CC=CC=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 170, 201, 201, 127, 127, 127, 127, 36, 5, 36, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 127, 201, 201, 201, 201, 184, 201, 201, 127, 36, 36, 36, 36, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 459 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003551 none CC1=CC=CC=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 93, 93, 127, 127, 105, 108, 127, 127, 127, 127, 1, 10, 10, 10, 10, 2, 10, 10, 1, 13, 13, 13, 13, 127, 127, 127, 127] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003551 none CC1=CC=CC=C1C1=NC=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 92, 92, 195, 195, 201, 201, 199, 201, 201, 201, 201, 201, 10, 2, 2, 2, 1, 1, 1, 1, 10, 92, 92, 92, 92, 201, 201, 201, 201] 201 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, 39, 40]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003551 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003551/1 /scratch/stefan/7769584/working/building/REAL300000003551 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/622 `/scratch/stefan/7769584/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=C2C)S1) `REAL300000003551.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003551 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 10, 75, 76, 156, 179, 179, 179, 179, 179, 179, 179, 179, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 76, 76, 76, 156, 179, 179, 179, 179, 10, 1, 1, 1, 1, 2, 2, 2] 179 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39, 40]) total number of confs: 467 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003551 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 13, 70, 114, 114, 96, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 13, 13, 13, 70, 114, 114, 114, 114, 1, 10, 10, 1, 10, 10, 10, 10] 179 rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 326 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003551 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 36, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 114, 114, 114, 114, 179, 179, 114, 179, 179, 179, 114, 36, 36, 36, 6, 1, 1, 1, 1, 114, 179, 179, 114, 179, 179, 179, 179] 179 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 9, 10, 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: 456 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003551 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003551 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003551/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003551/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003551 Building REAL300000003552 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003552' /scratch/stefan/7769584/working/building/REAL300000003552 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003552 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003552/0 /scratch/stefan/7769584/working/building/REAL300000003552 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/623 `/scratch/stefan/7769584/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CN=C(OC)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003552 none COCC1=CN=C(OC)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 126, 70, 70, 70, 70, 70, 70, 79, 36, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 129, 129, 129, 126, 126, 70, 79, 79, 79, 35, 6, 1, 1, 1, 1, 70] 129 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003552 none COCC1=CN=C(OC)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [33, 9, 1, 1, 1, 1, 1, 1, 3, 1, 1, 6, 6, 33, 70, 70, 36, 70, 70, 70, 70, 70, 1, 33, 33, 33, 9, 9, 1, 3, 3, 3, 6, 33, 70, 70, 70, 70, 1] 129 rigid atoms, others: [2, 3, 4, 5, 6, 7, 9, 10, 22, 38, 28] set([0, 1, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003552 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003552 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003552/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003552 Building REAL300000003553 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003553' /scratch/stefan/7769584/working/building/REAL300000003553 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003553 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003553/0 /scratch/stefan/7769584/working/building/REAL300000003553 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/624 `/scratch/stefan/7769584/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003553 none CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 26, 6, 1, 1, 1, 1] 34 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24]) 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: REAL300000003553 none CN1N=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 33, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 2, 2, 2, 1, 8, 33, 34, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003553 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003553 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003553/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003553 Building REAL300000003554 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003554' /scratch/stefan/7769584/working/building/REAL300000003554 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003554 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003554/0 /scratch/stefan/7769584/working/building/REAL300000003554 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/625 `/scratch/stefan/7769584/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003554 none COC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 196, 201, 201, 135, 26, 26, 64, 64, 26, 26, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 64, 64, 26, 6, 1, 1, 1, 1, 64, 64] 201 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 440 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003554 none COC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 16, 16, 16, 9, 16, 16, 5, 1, 1, 1, 1, 1, 1, 6, 6, 36, 64, 64, 36, 36, 64, 64, 64, 64, 1, 1, 29, 29, 29, 16, 16, 16, 16, 1, 1, 6, 36, 64, 64, 64, 64, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 43, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003554 none COC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 8, 8, 64, 64, 182, 201, 201, 182, 182, 201, 201, 201, 201, 16, 16, 4, 4, 4, 1, 1, 1, 1, 16, 16, 64, 182, 201, 201, 201, 201, 16, 16] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003554 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003554 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003554/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003554 Building REAL300000003555 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003555' /scratch/stefan/7769584/working/building/REAL300000003555 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003555 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003555/0 /scratch/stefan/7769584/working/building/REAL300000003555 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/626 `/scratch/stefan/7769584/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3N=CC=CN32)C=C1) `REAL300000003555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003555 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3N=CC=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 69, 73, 73, 64, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 73, 73, 73, 73, 64, 19, 1, 1, 1, 1, 1, 6, 6, 6, 73, 73] 73 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40]) total number of confs: 194 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003555 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3N=CC=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [72, 58, 72, 46, 72, 72, 43, 11, 11, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 43, 11, 6, 6, 1, 6, 6, 1, 1, 1, 72, 72] 73 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003555 none O=C([O-])C1=CC=C(NN=CC2=C(C3=CC=CC=C3)N=C3N=CC=CN32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 41, 42, 72, 72, 73, 73, 72, 73, 73, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 9, 41, 73, 73, 72, 73, 73, 72, 72, 72, 1, 1] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003555 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003555 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003555/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003555 Building REAL300000003556 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003556' /scratch/stefan/7769584/working/building/REAL300000003556 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003556 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003556/0 /scratch/stefan/7769584/working/building/REAL300000003556 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/627 `/scratch/stefan/7769584/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2CC2=CC=C(Cl)C=C2)C=C1) `REAL300000003556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003556 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2CC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 195, 201, 201, 195, 78, 78, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 195, 78, 18, 18, 18, 18, 5, 5, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41]) total number of confs: 543 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003556 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2CC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 78, 103, 74, 103, 103, 74, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 18, 103, 103, 103, 103, 74, 12, 1, 1, 1, 1, 10, 10, 18, 18, 18, 18, 103, 103] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003556 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2CC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 29, 29, 102, 102, 51, 102, 102, 102, 197, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 29, 102, 102, 102, 102, 197, 197, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003556 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003556 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003556/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003556 Building REAL300000003557 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003557' /scratch/stefan/7769584/working/building/REAL300000003557 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003557 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003557/0 /scratch/stefan/7769584/working/building/REAL300000003557 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/628 `/scratch/stefan/7769584/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(SC(F)(F)F)=C2)C=C1) `REAL300000003557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003557 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(SC(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [36, 36, 36, 20, 36, 36, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 1, 36, 36, 36, 36, 18, 4, 1, 1, 1, 1, 36, 36] 42 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003557 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(SC(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 32, 32, 88, 88, 88, 88, 88, 201, 201, 201, 201, 88, 1, 1, 1, 1, 9, 32, 88, 88, 88, 88, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003557 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003557 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003557/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003557 Building REAL300000003558 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003558' /scratch/stefan/7769584/working/building/REAL300000003558 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003558 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003558/0 /scratch/stefan/7769584/working/building/REAL300000003558 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/629 `/scratch/stefan/7769584/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3=CC=C(Cl)C=C3)=C2)C=C1) `REAL300000003558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003558 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations 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, 175, 61, 61, 20, 20, 20, 20, 20, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 175, 61, 20, 20, 20, 4, 4, 1, 1, 1, 1, 20, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41, 42]) total number of confs: 501 number of broken/clashed sets: 29 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003558 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens 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, 70, 118, 118, 62, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 11, 20, 20, 20, 20, 20, 20, 1, 118, 118, 118, 118, 62, 10, 1, 1, 1, 11, 11, 20, 20, 20, 20, 1, 118, 118] 201 rigid atoms, others: [32, 33, 40, 9, 10, 11, 12, 13, 14, 15, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 456 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: REAL300000003558 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3=CC=C(Cl)C=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 48, 48, 120, 120, 120, 120, 120, 177, 201, 201, 201, 201, 201, 201, 201, 120, 1, 1, 1, 1, 10, 48, 120, 120, 120, 201, 201, 201, 201, 201, 201, 120, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 399 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003558 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003558 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003558/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003558 Building REAL300000003559 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003559' /scratch/stefan/7769584/working/building/REAL300000003559 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003559 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003559/0 /scratch/stefan/7769584/working/building/REAL300000003559 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/630 `/scratch/stefan/7769584/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C3C(=C2)CCC32OCCO2)C=C1) `REAL300000003559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003559 none O=C([O-])C1=CC=C(NN=CC2=CC=C3C(=C2)CCC32OCCO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 35, 26, 35, 35, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 26, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 40, 23, 24, 25, 26, 27, 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: REAL300000003559 none O=C([O-])C1=CC=C(NN=CC2=CC=C3C(=C2)CCC32OCCO2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 8, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003559 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003559 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003559/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003559 Building REAL300000003560 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003560' /scratch/stefan/7769584/working/building/REAL300000003560 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003560 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003560/0 /scratch/stefan/7769584/working/building/REAL300000003560 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/631 `/scratch/stefan/7769584/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2OC(F)F)C=C1) `REAL300000003560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003560 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 44, 50, 29, 50, 50, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 50, 50, 50, 50, 29, 9, 1, 1, 1, 31, 50, 50] 65 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 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: REAL300000003560 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 35, 35, 70, 70, 36, 70, 70, 70, 70, 117, 139, 139, 1, 1, 1, 1, 9, 35, 70, 70, 70, 139, 1, 1] 139 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003560 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003560 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003560/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003560 Building REAL300000003561 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003561' /scratch/stefan/7769584/working/building/REAL300000003561 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003561 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003561/0 /scratch/stefan/7769584/working/building/REAL300000003561 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/632 `/scratch/stefan/7769584/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(N2CCCC2)=N1) `REAL300000003561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003561 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(N2CCCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 10, 67, 67, 150, 160, 160, 152, 160, 160, 160, 160, 160, 10, 1, 1, 1, 1, 1, 1, 10, 11, 11, 11, 67, 149, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 1] 160 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 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]) total number of confs: 454 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003561 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(N2CCCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [119, 119, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 118, 119, 160, 160, 160, 160, 119, 119, 119, 119, 39, 6, 1, 1, 1, 1, 160, 160, 160, 160, 160, 160, 160, 160] 160 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 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: REAL300000003561 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(N2CCCC2)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 78, 119, 119, 80, 95, 119, 119, 119, 119, 1, 1, 1, 10, 10, 10, 10, 1, 2, 2, 2, 12, 78, 119, 119, 119, 119, 10, 10, 10, 10, 10, 10, 10, 10] 160 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003561 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003561 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003561/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003561 Building REAL300000003562 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003562' /scratch/stefan/7769584/working/building/REAL300000003562 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003562 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003562/0 /scratch/stefan/7769584/working/building/REAL300000003562 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/633 `/scratch/stefan/7769584/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1) `REAL300000003562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003562 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [79, 12, 79, 145, 145, 147, 147, 147, 147, 147, 147, 147, 147, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 79, 79, 79, 79, 147, 147, 147, 147, 12, 1, 1, 1, 1] 147 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 355 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003562 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 84, 84, 104, 104, 89, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 13, 13, 13, 13, 104, 104, 104, 104, 1, 12, 12, 12, 12] 147 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003562 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [31, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 104, 104, 104, 104, 147, 147, 147, 147, 147, 104, 31, 31, 31, 31, 1, 1, 1, 1, 104, 147, 147, 147, 147] 147 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003562 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003562/1 /scratch/stefan/7769584/working/building/REAL300000003562 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/634 `/scratch/stefan/7769584/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1) `REAL300000003562.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003562 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [49, 13, 48, 49, 68, 79, 79, 68, 79, 79, 79, 79, 79, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 49, 49, 49, 68, 79, 79, 79, 79, 13, 1, 1, 1, 1] 79 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 243 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003562 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 40, 65, 65, 40, 47, 65, 65, 65, 65, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 12, 12, 12, 39, 65, 65, 65, 65, 1, 13, 13, 12, 13] 79 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 302 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003562 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 65, 65, 65, 65, 79, 79, 79, 79, 79, 65, 27, 27, 27, 6, 1, 1, 1, 1, 65, 79, 79, 79, 79] 79 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003562 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003562 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003562/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003562/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003562 Building REAL300000003563 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003563' /scratch/stefan/7769584/working/building/REAL300000003563 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003563 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003563/0 /scratch/stefan/7769584/working/building/REAL300000003563 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/635 `/scratch/stefan/7769584/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC2=CC(F)=CC=C12) `REAL300000003563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003563 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC2=CC(F)=CC=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 1, 15, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 27, 27, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 27, 7, 1, 1, 1, 1, 43, 43, 43] 43 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003563 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC2=CC(F)=CC=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 1, 15, 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, 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 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, 11, 11, 36, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 36, 43, 43, 43, 43, 1, 1, 1] 43 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003563 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003563 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003563/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003563 Building REAL300000003564 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003564' /scratch/stefan/7769584/working/building/REAL300000003564 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003564 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003564/0 /scratch/stefan/7769584/working/building/REAL300000003564 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/636 `/scratch/stefan/7769584/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=NC=C3)=NN2)C=C1) `REAL300000003564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003564 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=NC=C3)=NN2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 70, 71, 71, 69, 25, 24, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 7, 6, 71, 71, 71, 71, 70, 25, 7, 1, 1, 1, 1, 7, 71, 71] 71 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: 198 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003564 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=NC=C3)=NN2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [69, 43, 69, 40, 69, 69, 39, 8, 8, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 1, 1, 69, 69, 69, 69, 38, 8, 1, 7, 7, 7, 7, 1, 69, 69] 71 rigid atoms, others: [32, 9, 10, 11, 12, 13, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003564 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=NC=C3)=NN2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 37, 37, 69, 69, 69, 71, 71, 71, 71, 71, 69, 69, 1, 1, 1, 1, 10, 37, 69, 71, 71, 71, 71, 69, 1, 1] 71 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003564 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003564/1 /scratch/stefan/7769584/working/building/REAL300000003564 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/637 `/scratch/stefan/7769584/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NNC(C3=CC=NC=C3)=C2)C=C1) `REAL300000003564.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003564 none O=C([O-])C1=CC=C(NN=CC2=NNC(C3=CC=NC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 49, 54, 54, 49, 21, 21, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 54, 54, 54, 54, 49, 21, 6, 1, 1, 1, 1, 6, 54, 54] 54 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 160 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003564 none O=C([O-])C1=CC=C(NN=CC2=NNC(C3=CC=NC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [45, 33, 45, 27, 45, 45, 27, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 45, 45, 45, 45, 27, 7, 1, 6, 6, 6, 6, 1, 45, 45] 54 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34]) 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: REAL300000003564 none O=C([O-])C1=CC=C(NN=CC2=NNC(C3=CC=NC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 44, 44, 44, 44, 53, 53, 44, 53, 53, 44, 1, 1, 1, 1, 8, 34, 44, 53, 53, 53, 53, 44, 1, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003564 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003564 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003564/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003564/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003564 Building REAL300000003565 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003565' /scratch/stefan/7769584/working/building/REAL300000003565 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003565 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003565/0 /scratch/stefan/7769584/working/building/REAL300000003565 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/638 `/scratch/stefan/7769584/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1OC) `REAL300000003565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003565 none COC1=CC=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 119, 119, 119, 119, 119, 119, 33, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 141, 141, 141, 141, 119, 119, 32, 6, 1, 1, 1, 1, 141, 141, 141] 141 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003565 none COC1=CC=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 87, 119, 119, 111, 119, 119, 119, 119, 119, 1, 1, 6, 4, 4, 4, 1, 1, 13, 87, 119, 119, 119, 119, 6, 6, 6] 141 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003565 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003565 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003565/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003565 Building REAL300000003566 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003566' /scratch/stefan/7769584/working/building/REAL300000003566 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003566 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003566/0 /scratch/stefan/7769584/working/building/REAL300000003566 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/639 `/scratch/stefan/7769584/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=NC(Cl)=CC=C12) `REAL300000003566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003566 none COC1=CC(OC)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=NC(Cl)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 161, 161, 161, 161, 161, 187, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 161, 161, 161, 161, 161, 161, 161, 187, 187, 187, 161, 187, 187, 187, 40, 7, 1, 1, 1, 1, 161, 161] 187 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) 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: REAL300000003566 none COC1=CC(OC)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=NC(Cl)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 1, 1, 12, 12, 98, 161, 161, 98, 101, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 12, 98, 161, 161, 161, 161, 1, 1] 187 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 41, 40, 20, 21, 22, 23, 24, 25, 26, 30] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003566 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003566 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003566/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003566 Building REAL300000003567 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003567' /scratch/stefan/7769584/working/building/REAL300000003567 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003567 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003567/0 /scratch/stefan/7769584/working/building/REAL300000003567 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/640 `/scratch/stefan/7769584/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003567 none COC1=C(Br)C=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 95, 95, 95, 95, 72, 95, 95, 95, 35, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 94, 95, 35, 6, 1, 1, 1, 1] 97 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000003567 none COC1=C(Br)C=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 12, 12, 73, 95, 95, 73, 73, 95, 95, 95, 95, 3, 3, 3, 1, 1, 12, 73, 95, 95, 95, 95] 97 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003567 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003567 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003567/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003567 Building REAL300000003568 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003568' /scratch/stefan/7769584/working/building/REAL300000003568 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003568 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003568/0 /scratch/stefan/7769584/working/building/REAL300000003568 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/641 `/scratch/stefan/7769584/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C3OCCOC3=C(Br)S2)C=C1) `REAL300000003568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003568 none O=C([O-])C1=CC=C(NN=CC2=C3OCCOC3=C(Br)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 5, 5, 12, 1, 1, 17, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 3, 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, 31, 36, 31, 36, 36, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 36, 36, 30, 8, 1, 1, 1, 1, 35, 35] 36 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003568 none O=C([O-])C1=CC=C(NN=CC2=C3OCCOC3=C(Br)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 5, 5, 12, 1, 1, 17, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 8, 26, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003568 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003568 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003568/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003568 Building REAL300000003569 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003569' /scratch/stefan/7769584/working/building/REAL300000003569 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003569 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003569/0 /scratch/stefan/7769584/working/building/REAL300000003569 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/642 `/scratch/stefan/7769584/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C2SC=CN12) `REAL300000003569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003569 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C2SC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 14, 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, 2, 2, 7, 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: [12, 1, 12, 12, 26, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 38, 38, 38, 38, 1, 1, 1] 38 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003569 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C2SC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', '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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 14, 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, 2, 2, 7, 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: [27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 38, 38, 38, 38, 38, 38, 38, 28, 28, 28, 6, 1, 1, 1, 1, 38, 38, 38] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003569 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003569 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003569/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003569 Building REAL300000003570 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003570' /scratch/stefan/7769584/working/building/REAL300000003570 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003570 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003570/0 /scratch/stefan/7769584/working/building/REAL300000003570 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/643 `/scratch/stefan/7769584/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(S(N)(=O)=O)=C(C)S1) `REAL300000003570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003570 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(S(N)(=O)=O)=C(C)S1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'S.3', '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, 1, 11, 11, 1, 1, 1, 14, 8, 11, 11, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 35, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 84, 84, 84, 66, 66, 66, 66, 66, 66, 34, 6, 1, 1, 1, 1, 84, 84, 66, 66, 66] 84 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) 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: REAL300000003570 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(S(N)(=O)=O)=C(C)S1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'S.3', '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, 1, 11, 11, 1, 1, 1, 14, 8, 11, 11, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7, 41, 66, 66, 41, 53, 66, 66, 66, 66, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 7, 41, 66, 66, 66, 66, 5, 5, 2, 2, 2] 84 rigid atoms, others: [0, 1, 2, 3, 15, 16, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003570 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003570 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003570/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003570 Building REAL300000003571 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003571' /scratch/stefan/7769584/working/building/REAL300000003571 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003571 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003571/0 /scratch/stefan/7769584/working/building/REAL300000003571 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/644 `/scratch/stefan/7769584/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC=C1) `REAL300000003571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003571 none NS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 90, 105, 105, 91, 35, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 105, 105, 34, 6, 1, 1, 1, 1, 91, 91] 105 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 29, 30]) 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: REAL300000003571 none NS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 13, 13, 65, 91, 91, 65, 65, 91, 91, 91, 91, 1, 1, 1, 5, 5, 13, 65, 91, 91, 91, 91, 1, 1] 105 rigid atoms, others: [1, 4, 5, 6, 18, 19, 20, 29, 30] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003571 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003571 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003571/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003571 Building REAL300000003572 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003572' /scratch/stefan/7769584/working/building/REAL300000003572 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003572 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003572/0 /scratch/stefan/7769584/working/building/REAL300000003572 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/645 `/scratch/stefan/7769584/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NC2=CC=CC=C2N=C1) `REAL300000003572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003572 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 38, 38, 40, 40, 38, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 40, 40, 40, 40, 1, 1, 1, 1, 1] 40 rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 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: REAL300000003572 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 25, 40, 40, 40, 40, 40, 40, 40, 40, 40, 25, 25, 25, 25, 1, 1, 1, 1, 40, 40, 40, 40, 40] 40 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003572 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003572 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003572/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003572 Building REAL300000003573 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003573' /scratch/stefan/7769584/working/building/REAL300000003573 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003573 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003573/0 /scratch/stefan/7769584/working/building/REAL300000003573 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/646 `/scratch/stefan/7769584/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=COC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003573 none NS(=O)(=O)C1=COC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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, 78, 78, 39, 39, 39, 30, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 78, 78, 39, 29, 6, 1, 1, 1, 1, 39] 78 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 30]) 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: REAL300000003573 none NS(=O)(=O)C1=COC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 30, 39, 39, 30, 30, 39, 39, 39, 39, 1, 5, 5, 1, 7, 30, 39, 39, 39, 39, 1] 78 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 23, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003573 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003573/1 /scratch/stefan/7769584/working/building/REAL300000003573 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/647 `/scratch/stefan/7769584/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003573.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003573 none NS(=O)(=O)C1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 73, 185, 185, 73, 73, 73, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 185, 185, 73, 18, 18, 1, 1, 1, 1, 73] 185 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 30]) 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: REAL300000003573 none NS(=O)(=O)C1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 8, 60, 61, 73, 73, 62, 62, 73, 73, 73, 73, 1, 5, 5, 1, 8, 8, 73, 73, 73, 73, 1] 185 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 23, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003573 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003573 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003573/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003573/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003573 Building REAL300000003574 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003574' /scratch/stefan/7769584/working/building/REAL300000003574 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003574 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003574/0 /scratch/stefan/7769584/working/building/REAL300000003574 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/648 `/scratch/stefan/7769584/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CNC2=CC=CC=C12)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003574 none CC(CC1=CNC2=CC=CC=C12)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', '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, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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: [28, 4, 28, 58, 91, 91, 91, 91, 91, 91, 91, 91, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 58, 58, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1] 91 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 274 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: REAL300000003574 none CC(CC1=CNC2=CC=CC=C12)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', '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, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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: [24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 89, 89, 91, 91, 89, 89, 91, 91, 91, 91, 24, 24, 24, 24, 8, 8, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91] 91 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 29, 30, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003574 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003574 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003574/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003574 Building REAL300000003575 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003575' /scratch/stefan/7769584/working/building/REAL300000003575 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003575 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003575/0 /scratch/stefan/7769584/working/building/REAL300000003575 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/649 `/scratch/stefan/7769584/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=N2)N=C1C) `REAL300000003575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003575 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=N2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 1, 21, 21, 58, 80, 80, 58, 80, 80, 80, 80, 80, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 20, 21, 21, 58, 80, 80, 80, 80, 12, 1, 1, 1, 13, 13, 13] 80 rigid atoms, others: [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, 33, 34, 38, 39, 40]) total number of confs: 307 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003575 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=N2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 9, 9, 42, 76, 76, 42, 66, 76, 76, 76, 76, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 9, 9, 9, 42, 76, 76, 76, 76, 1, 6, 1, 6, 2, 2, 2] 80 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 330 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003575 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=C(C2=NC=CC=N2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 8, 1, 5, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 76, 76, 54, 54, 77, 77, 37, 77, 77, 76, 76, 76, 32, 32, 32, 5, 1, 1, 1, 1, 76, 77, 35, 77, 76, 76, 76] 80 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 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: 281 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003575 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003575 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003575/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003575 Building REAL300000003576 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003576' /scratch/stefan/7769584/working/building/REAL300000003576 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003576 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003576/0 /scratch/stefan/7769584/working/building/REAL300000003576 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/650 `/scratch/stefan/7769584/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(S(N)(=O)=O)=C1OC) `REAL300000003576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003576 none COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(S(N)(=O)=O)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 14, 8, 11, 11, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 6, 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: [111, 79, 79, 41, 41, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 78, 79, 148, 148, 148, 79, 79, 115, 111, 111, 111, 41, 6, 1, 1, 1, 1, 148, 148, 115, 115, 115] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 544 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: REAL300000003576 none COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(S(N)(=O)=O)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 14, 8, 11, 11, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 6, 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: [6, 1, 1, 1, 1, 13, 13, 56, 79, 79, 65, 79, 79, 79, 79, 79, 1, 1, 1, 4, 4, 4, 1, 1, 5, 6, 6, 6, 13, 56, 79, 79, 79, 79, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 16, 17, 18, 22, 23] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 268 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003576 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003576 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003576/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003576 Building REAL300000003577 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003577' /scratch/stefan/7769584/working/building/REAL300000003577 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003577 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003577/0 /scratch/stefan/7769584/working/building/REAL300000003577 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/651 `/scratch/stefan/7769584/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Cl)C=C2NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1) `REAL300000003577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003577 none COC1=C(Cl)C=C2NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 107, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 40, 7, 1, 1, 1, 1, 107] 107 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) 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: REAL300000003577 none COC1=C(Cl)C=C2NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 65, 107, 107, 69, 81, 107, 107, 107, 107, 1, 1, 4, 4, 4, 1, 1, 1, 12, 65, 107, 107, 107, 107, 1] 107 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 36, 27, 28, 29] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003577 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003577/1 /scratch/stefan/7769584/working/building/REAL300000003577 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/652 `/scratch/stefan/7769584/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Cl)C=C2NC=C(CN=NC3=CC=C(C(=O)[O-])C=C3)C2=C1) `REAL300000003577.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003577 none COC1=C(Cl)C=C2NC=C(CN=NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 84, 84, 84, 84, 26, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 26, 26, 1, 1, 1, 1, 84] 84 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 160 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003577 none COC1=C(Cl)C=C2NC=C(CN=NC3=CC=C(C(=O)[O-])C=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 68, 69, 84, 84, 69, 72, 84, 84, 84, 84, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 84, 84, 84, 84, 1] 84 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 36, 27, 28, 29] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003577 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003577 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003577/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003577/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003577 Building REAL300000003578 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003578' /scratch/stefan/7769584/working/building/REAL300000003578 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003578 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003578/0 /scratch/stefan/7769584/working/building/REAL300000003578 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/653 `/scratch/stefan/7769584/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2CC(N=NC3=CC=C(C(=O)[O-])C=C3)CCC2=C1) `REAL300000003578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003578 none COC1=CC=C2CC(N=NC3=CC=C(C(=O)[O-])C=C3)CCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11] 11 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003578 none COC1=CC=C2CC(N=NC3=CC=C(C(=O)[O-])C=C3)CCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 11, 10, 10, 11, 10, 11, 11, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 1, 1, 1] 11 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39] set([0, 32, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 31]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003578 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003578 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003578/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003578 Building REAL300000003579 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003579' /scratch/stefan/7769584/working/building/REAL300000003579 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003579 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003579/0 /scratch/stefan/7769584/working/building/REAL300000003579 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/654 `/scratch/stefan/7769584/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003579 none CN1C=CC(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 50, 50, 50, 50, 50, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 50, 50, 35, 7, 1, 1, 1, 1] 60 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003579 none CN1C=CC(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 50, 50, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 6, 30, 50, 50, 50, 50] 60 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 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: REAL300000003579 none CN1C=CC(C2=NNC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 12, 12, 21, 21, 58, 60, 60, 60, 60, 60, 60, 60, 60, 1, 2, 2, 2, 1, 1, 12, 12, 21, 58, 60, 60, 60, 60] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003579 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003579 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003579/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003579 Building REAL300000003580 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003580' /scratch/stefan/7769584/working/building/REAL300000003580 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003580 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003580/0 /scratch/stefan/7769584/working/building/REAL300000003580 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/655 `/scratch/stefan/7769584/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCC(=O)NC3=CC=C(Cl)C=C32)C=C1) `REAL300000003580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003580 none O=C([O-])C1=CC=C(NN=C2CCC(=O)NC3=CC=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 14, 8, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 14 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26, 36]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003580 none O=C([O-])C1=CC=C(NN=C2CCC(=O)NC3=CC=C(Cl)C=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 14 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003580 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003580 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003580/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003580 Building REAL300000003581 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003581' /scratch/stefan/7769584/working/building/REAL300000003581 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003581 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003581/0 /scratch/stefan/7769584/working/building/REAL300000003581 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/656 `/scratch/stefan/7769584/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=C1C) `REAL300000003581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003581 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 10, 1, 10, 10, 46, 61, 61, 49, 55, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 46, 61, 61, 61, 61, 1, 1, 1, 2, 2, 2] 67 rigid atoms, others: [32, 33, 2, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 264 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: REAL300000003581 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(Br)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 61, 61, 29, 29, 61, 61, 61, 49, 49, 49, 49, 49, 6, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61] 67 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 261 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003581 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003581 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003581/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003581 Building REAL300000003582 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003582' /scratch/stefan/7769584/working/building/REAL300000003582 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003582 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003582/0 /scratch/stefan/7769584/working/building/REAL300000003582 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/657 `/scratch/stefan/7769584/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003582 none CC1=CC=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', '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', '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, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 27, 43, 43, 43, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 42, 43, 25, 6, 1, 1, 1, 1] 43 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003582 none CC1=CC=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', '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', '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, 15, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 37, 43, 43, 37, 37, 43, 43, 43, 43, 1, 1, 2, 2, 2, 1, 1, 10, 37, 43, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003582 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003582 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003582/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003582 Building REAL300000003583 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003583' /scratch/stefan/7769584/working/building/REAL300000003583 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003583 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003583/0 /scratch/stefan/7769584/working/building/REAL300000003583 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/658 `/scratch/stefan/7769584/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCCC2CCCCC2)C=C1) `REAL300000003583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003583 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCCC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 199, 201, 201, 199, 128, 128, 97, 97, 97, 97, 97, 97, 32, 9, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 128, 97, 97, 97, 97, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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, 50, 51]) total number of confs: 549 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003583 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCCC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 14, 21, 14, 21, 21, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 53, 97, 97, 97, 97, 97, 21, 21, 21, 21, 14, 4, 1, 1, 1, 1, 33, 33, 69, 69, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 21, 21] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003583 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCCC2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 16, 16, 11, 16, 16, 16, 52, 125, 150, 201, 201, 201, 201, 201, 1, 1, 1, 1, 4, 11, 16, 16, 16, 16, 125, 125, 168, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 50, 51, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003583 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003583 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003583/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003583 Building REAL300000003584 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003584' /scratch/stefan/7769584/working/building/REAL300000003584 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003584 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003584/0 /scratch/stefan/7769584/working/building/REAL300000003584 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/659 `/scratch/stefan/7769584/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3CCC3)=C2)C=C1) `REAL300000003584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003584 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3CCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 201, 201, 198, 99, 99, 42, 42, 42, 42, 42, 29, 9, 1, 1, 1, 1, 1, 42, 201, 201, 201, 201, 198, 99, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 42, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 526 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003584 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3CCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens 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, 34, 43, 31, 43, 43, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 18, 42, 42, 42, 1, 43, 43, 43, 43, 30, 6, 1, 1, 1, 18, 18, 42, 42, 42, 42, 42, 42, 42, 1, 43, 43] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 276 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: REAL300000003584 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(OCC3CCC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 16, 16, 42, 42, 42, 42, 42, 88, 117, 201, 201, 201, 42, 1, 1, 1, 1, 4, 16, 42, 42, 42, 117, 117, 201, 201, 201, 201, 201, 201, 201, 42, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 557 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003584 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003584 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003584/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003584 Building REAL300000003585 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003585' /scratch/stefan/7769584/working/building/REAL300000003585 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003585 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003585/0 /scratch/stefan/7769584/working/building/REAL300000003585 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/660 `/scratch/stefan/7769584/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003585 none CC(F)(F)C1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 86, 96, 96, 86, 86, 46, 86, 86, 36, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 86, 59, 86, 86, 36, 6, 1, 1, 1, 1] 96 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]) 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: REAL300000003585 none CC(F)(F)C1=CC=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 60, 86, 86, 60, 60, 86, 86, 86, 86, 8, 8, 8, 1, 1, 1, 1, 10, 60, 86, 86, 86, 86] 96 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003585 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003585 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003585/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003585 Building REAL300000003586 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003586' /scratch/stefan/7769584/working/building/REAL300000003586 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003586 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003586/0 /scratch/stefan/7769584/working/building/REAL300000003586 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/661 `/scratch/stefan/7769584/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCCO) `REAL300000003586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003586 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCCO 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [95, 52, 52, 52, 18, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 139, 190, 201, 95, 95, 95, 52, 17, 3, 1, 1, 1, 1, 52, 52, 190, 190, 201, 201, 603] 603 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003586 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCCO 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 33, 52, 52, 33, 33, 52, 52, 52, 52, 1, 1, 1, 1, 9, 43, 73, 4, 4, 4, 1, 7, 33, 52, 52, 52, 52, 1, 1, 43, 43, 73, 73, 219] 603 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003586 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003586 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003586/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003586 Building REAL300000003587 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003587' /scratch/stefan/7769584/working/building/REAL300000003587 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003587 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003587/0 /scratch/stefan/7769584/working/building/REAL300000003587 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/662 `/scratch/stefan/7769584/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=NN2C)=N1) `REAL300000003587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003587 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=NN2C)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 50, 50, 120, 151, 151, 120, 121, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50, 120, 151, 151, 151, 151, 1, 1, 2, 2, 2] 151 rigid atoms, others: [34, 35, 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, 36, 37, 38]) total number of confs: 526 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003587 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=NN2C)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 96, 96, 151, 151, 151, 151, 151, 96, 96, 96, 96, 96, 33, 7, 1, 1, 1, 1, 151, 151, 151, 151, 151] 151 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) 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: REAL300000003587 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C2=CC=NN2C)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 63, 96, 96, 63, 64, 96, 96, 96, 96, 1, 1, 10, 10, 10, 10, 10, 1, 2, 2, 2, 1, 13, 63, 96, 96, 96, 96, 10, 10, 10, 10, 10] 151 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003587 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003587 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003587/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003587 Building REAL300000003588 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003588' /scratch/stefan/7769584/working/building/REAL300000003588 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003588 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003588/0 /scratch/stefan/7769584/working/building/REAL300000003588 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/663 `/scratch/stefan/7769584/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OCCO) `REAL300000003588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003588 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OCCO 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [82, 41, 41, 41, 41, 16, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 138, 187, 201, 82, 82, 82, 41, 41, 15, 3, 1, 1, 1, 1, 40, 187, 187, 201, 201, 603] 603 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 1209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003588 none COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1OCCO 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 40, 40, 24, 24, 40, 40, 40, 40, 1, 1, 1, 9, 41, 74, 4, 4, 4, 1, 1, 6, 24, 40, 40, 41, 41, 1, 41, 41, 74, 74, 222] 603 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 27, 28, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003588 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003588 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003588/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003588 Building REAL300000003589 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003589' /scratch/stefan/7769584/working/building/REAL300000003589 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003589 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003589/0 /scratch/stefan/7769584/working/building/REAL300000003589 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/664 `/scratch/stefan/7769584/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C([N+](=O)[O-])C=C1) `REAL300000003589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003589 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C([N+](=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1] 6 rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 15 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003589 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C([N+](=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 13 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003589 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C([N+](=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 6, 6, 6, 6, 1, 1, 1, 3, 3, 3, 3] 6 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 39, 15, 16, 17] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 32 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003589 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003589 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003589/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003589 Building REAL300000003590 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003590' /scratch/stefan/7769584/working/building/REAL300000003590 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003590 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003590/0 /scratch/stefan/7769584/working/building/REAL300000003590 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/665 `/scratch/stefan/7769584/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCC1CCCO1) `REAL300000003590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003590 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCC1CCCO1 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', '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.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 82, 82, 82, 82, 146, 146, 199, 201, 201, 199, 199, 201, 201, 201, 201, 82, 82, 25, 7, 1, 1, 1, 1, 1, 1, 125, 125, 125, 82, 146, 199, 201, 201, 201, 201, 82, 82, 7, 7, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003590 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCC1CCCO1 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', '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.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 13, 13, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 31, 31, 31, 102, 169, 201, 201, 201, 201, 57, 57, 57, 31, 13, 4, 1, 1, 1, 1, 31, 31, 169, 169, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 606 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003590 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC=C1OCC1CCCO1 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', '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.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 31, 31, 21, 21, 31, 31, 31, 31, 1, 1, 1, 1, 9, 42, 82, 82, 82, 82, 4, 4, 4, 1, 7, 21, 31, 31, 31, 31, 1, 1, 42, 42, 82, 82, 82, 82, 82, 82, 82] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 17, 18, 19, 20, 30, 37] set([0, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003590 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003590 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003590/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003590 Building REAL300000003591 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003591' /scratch/stefan/7769584/working/building/REAL300000003591 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003591 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003591/0 /scratch/stefan/7769584/working/building/REAL300000003591 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/666 `/scratch/stefan/7769584/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2C(F)(F)F)C=C1) `REAL300000003591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003591 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 26, 5, 1, 1, 1, 31, 31] 31 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003591 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(F)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 26, 26, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 10, 26, 31, 31, 31, 1, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003591 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003591 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003591/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003591 Building REAL300000003592 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003592' /scratch/stefan/7769584/working/building/REAL300000003592 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003592 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003592/0 /scratch/stefan/7769584/working/building/REAL300000003592 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/667 `/scratch/stefan/7769584/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC=C2OCC(F)(F)F)C=C1) `REAL300000003592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003592 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC=C2OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [108, 108, 108, 79, 108, 108, 74, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 108, 108, 108, 108, 74, 12, 1, 1, 1, 37, 37, 108, 108] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 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: REAL300000003592 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC=C2OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 29, 29, 86, 86, 86, 43, 86, 86, 86, 156, 201, 201, 201, 201, 1, 1, 1, 1, 10, 29, 86, 86, 86, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 636 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003592 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003592 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003592/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003592 Building REAL300000003593 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003593' /scratch/stefan/7769584/working/building/REAL300000003593 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003593 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003593/0 /scratch/stefan/7769584/working/building/REAL300000003593 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/668 `/scratch/stefan/7769584/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)N=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003593 none COC1=CC=C(Br)N=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 75, 28, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 28, 28, 1, 1, 1, 1] 76 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003593 none COC1=CC=C(Br)N=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 55, 55, 75, 75, 55, 55, 75, 75, 75, 75, 4, 4, 4, 1, 1, 7, 7, 75, 75, 75, 75] 76 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003593 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003593/1 /scratch/stefan/7769584/working/building/REAL300000003593 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/669 `/scratch/stefan/7769584/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)N=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003593.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003593 none COC1=CC=C(Br)N=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 8, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 103, 103, 103, 103, 103, 103, 103, 45, 44, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 103, 103, 44, 6, 1, 1, 1, 1] 109 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003593 none COC1=CC=C(Br)N=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 8, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 79, 103, 103, 79, 79, 103, 103, 103, 103, 4, 4, 4, 1, 1, 13, 79, 103, 103, 103, 103] 109 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003593 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003593 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003593/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003593/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003593 Building REAL300000003594 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003594' /scratch/stefan/7769584/working/building/REAL300000003594 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003594 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003594/0 /scratch/stefan/7769584/working/building/REAL300000003594 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/670 `/scratch/stefan/7769584/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)C1=CC=CC(Br)=C1) `REAL300000003594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003594 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 7, 21, 47, 47, 53, 53, 47, 49, 53, 53, 53, 53, 1, 7, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 21, 53, 53, 53, 53, 7, 7, 7, 7, 1, 1, 1, 1] 53 rigid atoms, others: [37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 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: REAL300000003594 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C(C)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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 33, 34, 53, 53, 53, 53, 53, 53, 23, 23, 23, 23, 23, 20, 1, 1, 1, 1, 34, 34, 34, 34, 53, 53, 53, 53] 53 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 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: 207 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003594 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003594 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003594/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003594 Building REAL300000003595 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003595' /scratch/stefan/7769584/working/building/REAL300000003595 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003595 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003595/0 /scratch/stefan/7769584/working/building/REAL300000003595 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/671 `/scratch/stefan/7769584/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CN=C1C(CC1=CC=C(F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003595 none CN1C=CN=C1C(CC1=CC=C(F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 24, 5, 24, 47, 49, 49, 47, 48, 49, 49, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 46, 46, 46, 46, 46, 24, 47, 47, 49, 49, 49, 49, 1, 1, 1, 1] 55 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 236 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003595 none CN1C=CN=C1C(CC1=CC=C(F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 24, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 49, 49, 37, 37, 49, 49, 49, 49, 24, 24, 24, 24, 24, 9, 4, 4, 1, 1, 1, 1, 49, 49, 49, 49] 55 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003595 none CN1C=CN=C1C(CC1=CC=C(F)C=C1)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 20, 24, 24, 20, 21, 24, 24, 9, 32, 32, 46, 46, 32, 32, 46, 46, 46, 46, 2, 2, 2, 1, 1, 9, 20, 20, 24, 24, 24, 24, 46, 46, 46, 46] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003595 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003595 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003595/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003595 Building REAL300000003596 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003596' /scratch/stefan/7769584/working/building/REAL300000003596 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003596 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003596/0 /scratch/stefan/7769584/working/building/REAL300000003596 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/672 `/scratch/stefan/7769584/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1OC) `REAL300000003596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003596 none COC1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [119, 99, 99, 99, 99, 39, 39, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 99, 99, 119, 119, 119, 119, 99, 39, 7, 1, 1, 1, 1, 119, 119, 119] 121 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 221 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: REAL300000003596 none COC1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 10, 10, 62, 99, 99, 63, 64, 98, 99, 99, 99, 1, 1, 6, 4, 4, 4, 1, 10, 62, 99, 99, 99, 99, 7, 7, 7] 121 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 430 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003596 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003596 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003596/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003596 Building REAL300000003597 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003597' /scratch/stefan/7769584/working/building/REAL300000003597 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003597 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003597/0 /scratch/stefan/7769584/working/building/REAL300000003597 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/673 `/scratch/stefan/7769584/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CN=C(C(F)F)S3)C=C2)C=C1) `REAL300000003597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003597 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CN=C(C(F)F)S3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 197, 199, 177, 193, 191, 132, 14, 12, 1, 1, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 196, 199, 194, 189, 131, 12, 12, 12, 1, 12, 12, 12, 198, 199] 199 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 574 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003597 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CN=C(C(F)F)S3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 52, 86, 86, 47, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 88, 88, 12, 1, 1, 86, 86, 86, 86, 46, 6, 1, 1, 12, 88, 1, 1, 86, 86] 199 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 560 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003597 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CN=C(C(F)F)S3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 14, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 42, 42, 86, 86, 42, 50, 191, 199, 199, 199, 199, 199, 191, 86, 86, 1, 1, 1, 1, 9, 42, 86, 86, 191, 199, 86, 86, 1, 1] 199 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003597 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003597 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003597/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003597 Building REAL300000003598 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003598' /scratch/stefan/7769584/working/building/REAL300000003598 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003598 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003598/0 /scratch/stefan/7769584/working/building/REAL300000003598 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/674 `/scratch/stefan/7769584/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Br)=C1O) `REAL300000003598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003598 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 17, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 33, 39, 39, 33, 33, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 33, 39, 39, 39, 39, 1, 2, 2, 2, 1, 2] 78 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35]) total number of confs: 149 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: REAL300000003598 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 17, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 39, 39, 39, 39, 39, 39, 39, 39, 26, 26, 26, 5, 1, 1, 1, 1, 39, 39, 39, 39, 39, 78] 78 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003598 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003598/1 /scratch/stefan/7769584/working/building/REAL300000003598 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/675 `/scratch/stefan/7769584/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Br)=C1[O-]) `REAL300000003598.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003598 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 17, 1, 12, 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, 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] 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, 3, 13, 21, 21, 13, 13, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 21, 21, 21, 21, 1, 2, 2, 2, 1] 21 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003598 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C)=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 17, 1, 12, 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, 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] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 21, 21, 21, 21, 21] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 34 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003598 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003598 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003598/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003598/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003598 Building REAL300000003599 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003599' /scratch/stefan/7769584/working/building/REAL300000003599 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003599 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003599/0 /scratch/stefan/7769584/working/building/REAL300000003599 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/676 `/scratch/stefan/7769584/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC3=C2OCO3)C=C1) `REAL300000003599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003599 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 37, 45, 37, 45, 45, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 37, 11, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 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: REAL300000003599 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 9, 25, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003599 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003599 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003599/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003599 Building REAL300000003600 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003600' /scratch/stefan/7769584/working/building/REAL300000003600 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003600 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003600/0 /scratch/stefan/7769584/working/building/REAL300000003600 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/677 `/scratch/stefan/7769584/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC=C1) `REAL300000003600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003600 none CS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 76, 78, 78, 76, 33, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 78, 78, 78, 32, 6, 1, 1, 1, 1, 76, 76] 78 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000003600 none CS(=O)(=O)C1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 1, 1, 1, 10, 10, 53, 76, 76, 53, 53, 76, 76, 76, 76, 1, 1, 1, 7, 7, 7, 10, 53, 76, 76, 76, 76, 1, 1] 78 rigid atoms, others: [1, 4, 5, 6, 18, 19, 20, 30, 31] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003600 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003600 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003600/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003600 Building REAL300000003601 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003601' /scratch/stefan/7769584/working/building/REAL300000003601 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003601 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003601/0 /scratch/stefan/7769584/working/building/REAL300000003601 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/678 `/scratch/stefan/7769584/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(OCC2=CC=CC=C2)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003601 none CC1=NN(C)C(OCC2=CC=CC=C2)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 94, 201, 201, 201, 201, 201, 201, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 201, 201, 201, 201, 201, 201, 201, 17, 5, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 598 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003601 none CC1=NN(C)C(OCC2=CC=CC=C2)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 18, 3, 1, 1, 1, 1, 1, 1, 1, 50, 50, 87, 87, 193, 201, 201, 193, 201, 201, 201, 201, 201, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 87, 193, 201, 201, 201, 201] 201 rigid atoms, others: [35, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003601 none CC1=NN(C)C(OCC2=CC=CC=C2)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 50, 50, 36, 50, 50, 1, 1, 9, 9, 37, 52, 52, 37, 37, 52, 52, 52, 52, 2, 2, 2, 2, 2, 2, 29, 29, 50, 50, 50, 50, 50, 9, 37, 52, 52, 52, 52] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 14, 15] set([7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003601 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003601 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003601/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003601 Building REAL300000003602 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003602' /scratch/stefan/7769584/working/building/REAL300000003602 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003602 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003602/0 /scratch/stefan/7769584/working/building/REAL300000003602 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/679 `/scratch/stefan/7769584/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=COC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003602 none CS(=O)(=O)C1=COC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 49, 63, 63, 49, 49, 49, 32, 32, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 63, 63, 63, 49, 32, 7, 1, 1, 1, 1, 49] 63 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003602 none CS(=O)(=O)C1=COC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 39, 49, 49, 41, 48, 49, 49, 49, 49, 1, 3, 3, 3, 1, 6, 38, 49, 49, 49, 49, 1] 63 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 24, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003602 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003602/1 /scratch/stefan/7769584/working/building/REAL300000003602 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/680 `/scratch/stefan/7769584/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003602.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003602 none CS(=O)(=O)C1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 78, 95, 95, 78, 78, 78, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 95, 95, 95, 78, 18, 18, 1, 1, 1, 1, 78] 95 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003602 none CS(=O)(=O)C1=COC(CN=NC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 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 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, 3, 1, 1, 1, 1, 1, 8, 65, 66, 78, 78, 67, 67, 78, 78, 78, 78, 1, 3, 3, 3, 1, 8, 8, 78, 78, 78, 78, 1] 95 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 24, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003602 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003602 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003602/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003602/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003602 Building REAL300000003603 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003603' /scratch/stefan/7769584/working/building/REAL300000003603 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003603 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003603/0 /scratch/stefan/7769584/working/building/REAL300000003603 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/681 `/scratch/stefan/7769584/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2F)C=C1) `REAL300000003603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003603 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 21, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 21, 6, 1, 1, 1, 26, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003603 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 22, 22, 27, 27, 26, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 22, 27, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003603 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003603 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003603/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003603 Building REAL300000003604 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003604' /scratch/stefan/7769584/working/building/REAL300000003604 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003604 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003604/0 /scratch/stefan/7769584/working/building/REAL300000003604 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/682 `/scratch/stefan/7769584/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F) `REAL300000003604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003604 none CC(C)OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 109, 109, 109, 109, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 188, 188, 188, 188, 188, 188, 188, 109, 108, 37, 6, 1, 1, 1, 1, 109] 188 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 277 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: REAL300000003604 none CC(C)OC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 33, 1, 1, 1, 1, 1, 1, 10, 10, 66, 108, 108, 72, 108, 108, 108, 108, 108, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 1, 1, 10, 66, 108, 109, 108, 108, 1] 188 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 22, 38, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 467 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003604 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003604 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003604/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003604 Building REAL300000003605 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003605' /scratch/stefan/7769584/working/building/REAL300000003605 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003605 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003605/0 /scratch/stefan/7769584/working/building/REAL300000003605 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/683 `/scratch/stefan/7769584/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCCC(C3CCCCC3)C2)C=C1) `REAL300000003605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003605 none O=C([O-])C1=CC=C(N=NC2CCCC(C3CCCCC3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 16, 17, 17, 16, 16, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17] 17 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47]) total number of confs: 37 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003605 none O=C([O-])C1=CC=C(N=NC2CCCC(C3CCCCC3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 8, 6, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 9, 9] 17 rigid atoms, others: [32, 45, 8, 9, 10, 11, 12, 13, 14, 44, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) 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: REAL300000003605 none O=C([O-])C1=CC=C(N=NC2CCCC(C3CCCCC3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 1, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003605 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003605 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003605/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003605 Building REAL300000003606 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003606' /scratch/stefan/7769584/working/building/REAL300000003606 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003606 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003606/0 /scratch/stefan/7769584/working/building/REAL300000003606 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/684 `/scratch/stefan/7769584/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1F) `REAL300000003606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003606 none COC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 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, 52, 83, 52, 52, 52, 52, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 83, 83, 83, 52, 52, 52, 30, 6, 1, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003606 none COC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 9, 38, 52, 52, 40, 48, 52, 52, 52, 52, 1, 1, 13, 13, 13, 1, 1, 1, 9, 38, 52, 52, 52, 52] 83 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 22, 26, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003606 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003606 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003606/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003606 Building REAL300000003607 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003607' /scratch/stefan/7769584/working/building/REAL300000003607 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003607 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003607/0 /scratch/stefan/7769584/working/building/REAL300000003607 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/685 `/scratch/stefan/7769584/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC2=C1OCC2) `REAL300000003607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003607 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [32, 12, 1, 12, 12, 62, 104, 104, 85, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 62, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1] 115 rigid atoms, others: [2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 390 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: REAL300000003607 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [60, 30, 30, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 104, 104, 104, 104, 104, 104, 104, 104, 104, 60, 60, 60, 60, 60, 6, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104] 115 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 12, 13, 30, 31] set([0, 1, 2, 3, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 286 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003607 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003607/1 /scratch/stefan/7769584/working/building/REAL300000003607 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/686 `/scratch/stefan/7769584/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC2=C1OCC2) `REAL300000003607.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003607 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 13, 1, 13, 55, 55, 76, 76, 55, 57, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 13, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1] 76 rigid atoms, others: [2, 35, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000003607 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 23, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 23, 76, 76, 76, 76, 76, 76, 76, 76, 76, 32, 32, 32, 32, 32, 23, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76] 76 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 12, 13, 30, 31] set([0, 1, 2, 3, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003607 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003607 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003607/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003607/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003607 Building REAL300000003608 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003608' /scratch/stefan/7769584/working/building/REAL300000003608 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003608 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003608/0 /scratch/stefan/7769584/working/building/REAL300000003608 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/687 `/scratch/stefan/7769584/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC(CC2CCCC2)CC2CCCC2)C=C1) `REAL300000003608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003608 none O=C([O-])C1=CC=C(N=NC(CC2CCCC2)CC2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [102, 82, 102, 82, 102, 102, 80, 80, 21, 5, 21, 55, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 21, 56, 56, 81, 81, 81, 81, 81, 81, 81, 81, 81, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 102] 134 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 572 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003608 none O=C([O-])C1=CC=C(N=NC(CC2CCCC2)CC2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [92, 74, 92, 74, 92, 92, 73, 73, 17, 5, 1, 1, 1, 1, 1, 1, 17, 55, 81, 81, 81, 81, 92, 92, 92, 92, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 81, 81, 81, 81, 81, 81, 81, 81, 81, 92, 92] 134 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 534 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: REAL300000003608 none O=C([O-])C1=CC=C(N=NC(CC2CCCC2)CC2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 25, 54, 83, 83, 83, 83, 25, 62, 83, 83, 83, 83, 1, 1, 1, 1, 25, 57, 57, 83, 83, 83, 83, 83, 83, 83, 83, 83, 64, 64, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 49, 50, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 557 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003608 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003608 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003608/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003608 Building REAL300000003609 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003609' /scratch/stefan/7769584/working/building/REAL300000003609 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003609 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003609/0 /scratch/stefan/7769584/working/building/REAL300000003609 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/688 `/scratch/stefan/7769584/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C3=CC=CC=C3C=C2)C=C1) `REAL300000003609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003609 none O=C([O-])C1=CC=C(NN=CC2=C(F)C3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 20, 25, 20, 25, 25, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 20, 7, 1, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 21, 22, 23, 24, 25, 26]) 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: REAL300000003609 none O=C([O-])C1=CC=C(NN=CC2=C(F)C3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 10, 24, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003609 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003609 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003609/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003609 Building REAL300000003610 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003610' /scratch/stefan/7769584/working/building/REAL300000003610 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003610 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003610/0 /scratch/stefan/7769584/working/building/REAL300000003610 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/689 `/scratch/stefan/7769584/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003610 none CS(=O)(=O)C1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 61, 81, 81, 61, 61, 61, 34, 34, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 61, 81, 81, 81, 61, 34, 7, 1, 1, 1, 1, 61] 81 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003610 none CS(=O)(=O)C1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 12, 12, 48, 61, 61, 59, 61, 61, 61, 61, 61, 1, 3, 3, 3, 1, 12, 48, 61, 61, 61, 61, 1] 81 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 24, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003610 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003610 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003610/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003610 Building REAL300000003611 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003611' /scratch/stefan/7769584/working/building/REAL300000003611 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003611 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003611/0 /scratch/stefan/7769584/working/building/REAL300000003611 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/690 `/scratch/stefan/7769584/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(Cl)=C3)N=C2)C=C1) `REAL300000003611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003611 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(Cl)=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 86, 100, 100, 80, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 100, 100, 100, 100, 80, 25, 7, 1, 1, 1, 1, 7, 100, 100] 100 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 288 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003611 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(Cl)=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [75, 66, 75, 47, 75, 75, 47, 7, 7, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 75, 75, 75, 75, 47, 7, 1, 7, 7, 6, 7, 1, 75, 75] 100 rigid atoms, others: [33, 9, 10, 11, 12, 13, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 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: REAL300000003611 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(Cl)=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 11, 39, 39, 78, 78, 78, 102, 102, 102, 102, 102, 102, 78, 78, 1, 1, 1, 1, 11, 39, 78, 102, 102, 102, 102, 78, 1, 1] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003611 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003611 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003611/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003611 Building REAL300000003612 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003612' /scratch/stefan/7769584/working/building/REAL300000003612 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003612 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003612/0 /scratch/stefan/7769584/working/building/REAL300000003612 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/691 `/scratch/stefan/7769584/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCCC2)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003612 none CC1=NN(C2CCCC2)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 141, 141, 141, 141, 44, 44, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 104, 104, 104, 104, 141, 141, 141, 141, 141, 141, 141, 141, 141, 44, 7, 1, 1, 1, 1, 104] 141 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 284 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003612 none CC1=NN(C2CCCC2)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 7, 40, 40, 132, 141, 141, 132, 132, 141, 141, 141, 141, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 132, 141, 141, 141, 141, 6] 141 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000003612 none CC1=NN(C2CCCC2)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 11, 11, 71, 104, 104, 71, 72, 104, 104, 104, 104, 1, 2, 2, 2, 6, 7, 7, 6, 7, 7, 7, 6, 6, 11, 71, 104, 104, 104, 104, 1] 141 rigid atoms, others: [0, 1, 2, 3, 4, 9, 10, 22, 41] set([5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003612 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003612 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003612/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003612 Building REAL300000003613 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003613' /scratch/stefan/7769584/working/building/REAL300000003613 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003613 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003613/0 /scratch/stefan/7769584/working/building/REAL300000003613 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/692 `/scratch/stefan/7769584/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Br)C=C(C(F)(F)F)S2)C=C1) `REAL300000003613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003613 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=C(C(F)(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 44, 44, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 43, 44, 44, 44, 35, 12, 1, 43, 44] 44 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28]) 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: REAL300000003613 none O=C([O-])C1=CC=C(NN=CC2=C(Br)C=C(C(F)(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 23, 23, 43, 44, 43, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 9, 23, 43, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003613 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003613 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003613/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003613 Building REAL300000003614 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003614' /scratch/stefan/7769584/working/building/REAL300000003614 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003614 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003614/0 /scratch/stefan/7769584/working/building/REAL300000003614 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/693 `/scratch/stefan/7769584/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003614 none N#CC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 26, 6, 1, 1, 1, 1] 55 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003614 none N#CC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 47, 55, 55, 47, 47, 55, 55, 55, 55, 1, 1, 1, 12, 47, 55, 55, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003614 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003614/1 /scratch/stefan/7769584/working/building/REAL300000003614 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/694 `/scratch/stefan/7769584/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(Br)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003614.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003614 none N#CC1=CC=C(Br)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 15, 15, 1, 1, 1, 1] 38 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003614 none N#CC1=CC=C(Br)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 7, 7, 38, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003614 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003614 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003614/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003614/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003614 Building REAL300000003615 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003615' /scratch/stefan/7769584/working/building/REAL300000003615 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003615 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003615/0 /scratch/stefan/7769584/working/building/REAL300000003615 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/695 `/scratch/stefan/7769584/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Cl)=N2)C=C1) `REAL300000003615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003615 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Cl)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 21, 25, 25, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 21, 6, 1, 1, 25, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003615 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Cl)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 21, 21, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 9, 21, 24, 24, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003615 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003615/1 /scratch/stefan/7769584/working/building/REAL300000003615 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/696 `/scratch/stefan/7769584/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CC(Cl)=CC(Cl)=N2)C=C1) `REAL300000003615.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003615 none O=C([O-])C1=CC=C(N=NCC2=CC(Cl)=CC(Cl)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 9, 9, 1, 1, 47, 47] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003615 none O=C([O-])C1=CC=C(N=NCC2=CC(Cl)=CC(Cl)=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 18, 18, 47, 47, 1, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003615 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003615 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003615/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003615/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003615 Building REAL300000003616 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003616' /scratch/stefan/7769584/working/building/REAL300000003616 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003616 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003616/0 /scratch/stefan/7769584/working/building/REAL300000003616 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/697 `/scratch/stefan/7769584/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NC=CC3=CC(Cl)=CC=C32)C=C1) `REAL300000003616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003616 none O=C([O-])C1=CC=C(NN=CC2=NC=CC3=CC(Cl)=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 55, 63, 63, 54, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 54, 12, 1, 1, 1, 1, 1, 63, 63] 63 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26]) 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: REAL300000003616 none O=C([O-])C1=CC=C(NN=CC2=NC=CC3=CC(Cl)=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 33, 33, 63, 63, 62, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 9, 33, 63, 62, 63, 63, 63, 1, 1] 63 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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/7769584/working/building/REAL300000003616 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003616/1 /scratch/stefan/7769584/working/building/REAL300000003616 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/698 `/scratch/stefan/7769584/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NC=CC3=CC(Cl)=CC=C32)C=C1) `REAL300000003616.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003616 none O=C([O-])C1=CC=C(N=NCC2=NC=CC3=CC(Cl)=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 8, 8, 1, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26]) total number of confs: 60 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: REAL300000003616 none O=C([O-])C1=CC=C(N=NCC2=NC=CC3=CC(Cl)=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 16, 16, 36, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003616 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003616 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003616/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003616/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003616 Building REAL300000003617 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003617' /scratch/stefan/7769584/working/building/REAL300000003617 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003617 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003617/0 /scratch/stefan/7769584/working/building/REAL300000003617 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/699 `/scratch/stefan/7769584/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2OC2CC2)C=C1) `REAL300000003617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003617 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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, 121, 122, 122, 119, 69, 69, 42, 42, 42, 42, 42, 42, 42, 9, 1, 1, 1, 1, 122, 122, 122, 122, 119, 69, 42, 42, 42, 1, 1, 1, 1, 1, 122, 122] 122 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 297 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003617 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [75, 48, 75, 47, 75, 75, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 42, 42, 75, 75, 75, 75, 41, 12, 1, 1, 1, 42, 42, 42, 42, 42, 74, 75] 122 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 397 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003617 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 33, 56, 56, 35, 56, 56, 56, 56, 84, 92, 92, 1, 1, 1, 1, 7, 32, 56, 56, 56, 92, 92, 92, 92, 92, 1, 1] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 251 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003617 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003617 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003617/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003617 Building REAL300000003618 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003618' /scratch/stefan/7769584/working/building/REAL300000003618 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003618 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003618/0 /scratch/stefan/7769584/working/building/REAL300000003618 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/700 `/scratch/stefan/7769584/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C([N+](=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003618 none CN(C)C1=CC=C([N+](=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 29, 7, 1, 1, 1, 1] 37 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 62 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003618 none CN(C)C1=CC=C([N+](=O)[O-])C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 29, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 1, 1, 1, 8, 29, 37, 37, 37, 37] 37 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 30, 31] set([0, 2, 8, 9, 13, 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: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003618 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003618 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003618/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003618 Building REAL300000003619 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003619' /scratch/stefan/7769584/working/building/REAL300000003619 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003619 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003619/0 /scratch/stefan/7769584/working/building/REAL300000003619 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/701 `/scratch/stefan/7769584/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(Cl)=C2C(F)(F)F)C=C1) `REAL300000003619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003619 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Cl)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 31, 31, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 26, 5, 1, 1, 1, 31, 31] 31 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003619 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Cl)=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 11, 27, 32, 32, 32, 1, 1] 32 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003619 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003619 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003619/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003619 Building REAL300000003620 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003620' /scratch/stefan/7769584/working/building/REAL300000003620 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003620 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003620/0 /scratch/stefan/7769584/working/building/REAL300000003620 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/702 `/scratch/stefan/7769584/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(Br)=C2Cl)C=C1) `REAL300000003620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003620 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(Br)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 46, 40, 46, 46, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 40, 11, 1, 1, 46, 46] 46 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: REAL300000003620 none O=C([O-])C1=CC=C(NN=CC2=C(F)C=CC(Br)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 27, 27, 46, 46, 46, 43, 46, 46, 46, 46, 1, 1, 1, 1, 9, 27, 46, 36, 1, 1] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003620 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003620 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003620/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003620 Building REAL300000003621 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003621' /scratch/stefan/7769584/working/building/REAL300000003621 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003621 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003621/0 /scratch/stefan/7769584/working/building/REAL300000003621 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/703 `/scratch/stefan/7769584/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CN=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003621 none CN(C)C1=CN=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 42, 49, 49, 49, 28, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 27, 6, 1, 1, 1, 1] 49 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 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: REAL300000003621 none CN(C)C1=CN=CC(F)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 49, 49, 44, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 1, 1, 12, 44, 49, 49, 49, 49] 49 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003621 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003621 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003621/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003621 Building REAL300000003622 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003622' /scratch/stefan/7769584/working/building/REAL300000003622 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003622 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003622/0 /scratch/stefan/7769584/working/building/REAL300000003622 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/704 `/scratch/stefan/7769584/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(F)=C3)N=C2)C=C1) `REAL300000003622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003622 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(F)=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 87, 99, 99, 81, 28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 99, 99, 99, 99, 81, 28, 7, 1, 1, 1, 1, 7, 99, 99] 99 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 280 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003622 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(F)=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [82, 69, 82, 52, 82, 82, 52, 9, 9, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 82, 82, 82, 82, 52, 9, 1, 7, 7, 6, 7, 1, 82, 82] 99 rigid atoms, others: [33, 9, 10, 11, 12, 13, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 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: REAL300000003622 none O=C([O-])C1=CC=C(NN=CC2=CN(C3=CC=CC(F)=C3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 43, 43, 82, 82, 82, 99, 99, 99, 99, 99, 99, 82, 82, 1, 1, 1, 1, 11, 43, 82, 99, 99, 99, 99, 82, 1, 1] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003622 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003622 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003622/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003622 Building REAL300000003623 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003623' /scratch/stefan/7769584/working/building/REAL300000003623 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003623 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003623/0 /scratch/stefan/7769584/working/building/REAL300000003623 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/705 `/scratch/stefan/7769584/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Cl) `REAL300000003623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003623 none COC1=NC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 30, 6, 1, 1, 1, 1, 58, 58, 58] 58 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) 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: REAL300000003623 none COC1=NC(C)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 58, 58, 49, 58, 58, 58, 58, 58, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 9, 49, 58, 58, 58, 58, 2, 2, 2] 58 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003623 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003623 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003623/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003623 Building REAL300000003624 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003624' /scratch/stefan/7769584/working/building/REAL300000003624 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003624 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003624/0 /scratch/stefan/7769584/working/building/REAL300000003624 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/706 `/scratch/stefan/7769584/working/3D/706' -> `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(C(=O)[O-])C=C2)C(O)=C1) `REAL300000003624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003624 none CC(C)N(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(O)=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 226 conformations in input total number of sets (complete confs): 226 using faster count positions algorithm for large data unique positions, atoms: [113, 109, 113, 47, 109, 31, 47, 47, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 113, 113, 113, 113, 113, 113, 113, 109, 109, 109, 47, 47, 30, 6, 1, 1, 1, 1, 94, 47] 226 rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 442 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: REAL300000003624 none CC(C)N(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(O)=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 226 conformations in input total number of sets (complete confs): 226 using faster count positions algorithm for large data unique positions, atoms: [39, 11, 39, 1, 11, 1, 1, 1, 1, 1, 4, 4, 24, 47, 47, 24, 24, 47, 47, 47, 47, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 1, 1, 4, 24, 47, 47, 47, 47, 2, 1] 226 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 43, 35, 21, 22, 23] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 340 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003624 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003624 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003624/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003624 Building REAL300000003625 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003625' /scratch/stefan/7769584/working/building/REAL300000003625 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003625 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003625/0 /scratch/stefan/7769584/working/building/REAL300000003625 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/707 `/scratch/stefan/7769584/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC3=C2OCO3)C=C1) `REAL300000003625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003625 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [38, 32, 38, 31, 38, 38, 31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 31, 12, 2, 1, 1, 1, 1, 38, 38] 76 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 129 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: REAL300000003625 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 26, 38, 38, 38, 37, 38, 38, 38, 38, 38, 1, 1, 1, 1, 8, 25, 76, 38, 38, 38, 38, 1, 1] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003625 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003625 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003625/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003625 Building REAL300000003626 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003626' /scratch/stefan/7769584/working/building/REAL300000003626 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003626 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003626/0 /scratch/stefan/7769584/working/building/REAL300000003626 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/708 `/scratch/stefan/7769584/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C([O-])C=C2F)C=C1) `REAL300000003626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003626 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C([O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 17, 1, 12, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 16, 17, 17, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 15, 7, 1, 1, 17, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003626 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C([O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 17, 1, 12, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 17, 17, 17, 15, 17, 17, 17, 17, 1, 1, 1, 1, 6, 15, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003626 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003626/1 /scratch/stefan/7769584/working/building/REAL300000003626 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/709 `/scratch/stefan/7769584/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C(O)C=C2F)C=C1) `REAL300000003626.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003626 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C(O)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 12, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 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: [24, 24, 24, 20, 24, 24, 20, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 20, 8, 1, 2, 1, 24, 24] 48 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 26, 28, 29]) 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: REAL300000003626 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=C(O)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 12, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 24, 24, 24, 20, 24, 24, 24, 24, 1, 1, 1, 1, 9, 20, 24, 48, 24, 1, 1] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003626 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003626 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003626/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003626/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003626 Building REAL300000003627 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003627' /scratch/stefan/7769584/working/building/REAL300000003627 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003627 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003627/0 /scratch/stefan/7769584/working/building/REAL300000003627 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/710 `/scratch/stefan/7769584/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(O)=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003627 none COC1=CC(O)=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 62, 62, 62, 38, 62, 62, 62, 62, 38, 38, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 62, 62, 62, 62, 124, 62, 38, 7, 1, 1, 1, 1] 124 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003627 none COC1=CC(O)=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 44, 62, 62, 51, 62, 62, 62, 62, 62, 3, 3, 3, 1, 2, 1, 11, 44, 62, 62, 62, 62] 124 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 27] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003627 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003627/1 /scratch/stefan/7769584/working/building/REAL300000003627 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/711 `/scratch/stefan/7769584/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC([O-])=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003627.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003627 none COC1=CC([O-])=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 34, 24, 24, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 34, 34, 34, 34, 24, 6, 1, 1, 1, 1] 34 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003627 none COC1=CC([O-])=C(Cl)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 34, 34, 31, 34, 34, 34, 34, 34, 4, 4, 4, 1, 1, 10, 30, 34, 34, 34, 34] 34 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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/7769584/working/building/REAL300000003627 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003627 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003627/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003627/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003627 Building REAL300000003628 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003628' /scratch/stefan/7769584/working/building/REAL300000003628 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003628 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003628/0 /scratch/stefan/7769584/working/building/REAL300000003628 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/712 `/scratch/stefan/7769584/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)N=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003628 none CC1=NN(C2=CC=CC=C2)N=C1C=NNC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 36, 36, 36, 36, 36, 36, 36, 36, 36, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 22, 6, 1, 1, 1, 1] 36 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 62 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003628 none CC1=NN(C2=CC=CC=C2)N=C1C=NNC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 29, 36, 36, 29, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 1, 1, 1, 9, 29, 36, 36, 36, 36] 36 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 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, 32, 33, 34, 35, 36, 37]) 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: REAL300000003628 none CC1=NN(C2=CC=CC=C2)N=C1C=NNC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 2, 2, 2, 1, 1, 1, 8, 8, 28, 35, 35, 28, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 8, 28, 35, 35, 35, 35] 36 rigid atoms, others: [0, 1, 2, 3, 4, 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, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003628 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003628/1 /scratch/stefan/7769584/working/building/REAL300000003628 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/713 `/scratch/stefan/7769584/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)N=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003628.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003628 none CC1=NN(C2=CC=CC=C2)N=C1CN=NC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 21, 21, 1, 1, 1, 1] 47 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003628 none CC1=NN(C2=CC=CC=C2)N=C1CN=NC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 1, 1, 1, 1, 1, 13, 13, 47, 47, 47, 47] 47 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 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, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003628 none CC1=NN(C2=CC=CC=C2)N=C1CN=NC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 3, 3, 2, 3, 3, 1, 1, 1, 9, 43, 43, 47, 47, 43, 47, 47, 47, 47, 47, 2, 2, 2, 3, 3, 2, 3, 3, 9, 9, 47, 47, 47, 47] 47 rigid atoms, others: [0, 1, 2, 3, 4, 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, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003628 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003628 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003628/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003628/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003628 Building REAL300000003629 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003629' /scratch/stefan/7769584/working/building/REAL300000003629 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003629 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003629/0 /scratch/stefan/7769584/working/building/REAL300000003629 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/714 `/scratch/stefan/7769584/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NN(C3CC3(F)F)C=C2)C=C1) `REAL300000003629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003629 none O=C([O-])C1=CC=C(N=NCC2=NN(C3CC3(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 201, 200, 200, 62, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 201, 201, 201, 201, 62, 62, 1, 1, 1, 12, 12, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003629 none O=C([O-])C1=CC=C(N=NCC2=NN(C3CC3(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 76, 63, 76, 76, 63, 63, 9, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 76, 76, 76, 76, 9, 9, 12, 12, 12, 1, 1, 76, 76] 201 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) 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: REAL300000003629 none O=C([O-])C1=CC=C(N=NCC2=NN(C3CC3(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 32, 86, 86, 86, 201, 201, 201, 201, 86, 86, 1, 1, 1, 1, 32, 32, 201, 201, 201, 86, 86, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003629 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003629/1 /scratch/stefan/7769584/working/building/REAL300000003629 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/715 `/scratch/stefan/7769584/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NN(C3CC3(F)F)C=C2)C=C1) `REAL300000003629.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003629 none O=C([O-])C1=CC=C(NN=CC2=NN(C3CC3(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 62, 78, 62, 78, 78, 62, 30, 30, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 78, 78, 78, 78, 62, 30, 1, 1, 1, 13, 13, 78, 78] 78 rigid atoms, others: [12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003629 none O=C([O-])C1=CC=C(NN=CC2=NN(C3CC3(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [49, 34, 49, 34, 49, 49, 34, 8, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 49, 49, 49, 49, 34, 8, 13, 13, 13, 1, 1, 49, 49] 78 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) 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: REAL300000003629 none O=C([O-])C1=CC=C(NN=CC2=NN(C3CC3(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 33, 33, 46, 46, 46, 69, 69, 69, 69, 46, 46, 1, 1, 1, 1, 10, 33, 69, 69, 69, 46, 46, 1, 1] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003629 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003629 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003629/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003629/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003629 Building REAL300000003630 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003630' /scratch/stefan/7769584/working/building/REAL300000003630 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003630 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003630/0 /scratch/stefan/7769584/working/building/REAL300000003630 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/716 `/scratch/stefan/7769584/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003630 none CC1=NN(C2CCCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 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: [87, 87, 87, 87, 87, 201, 201, 201, 201, 201, 87, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 39, 6, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003630 none CC1=NN(C2CCCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 65, 65, 175, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 65, 175, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 37, 35, 36, 27, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003630 none CC1=NN(C2CCCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 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, 13, 13, 13, 13, 13, 1, 1, 1, 10, 10, 50, 86, 86, 57, 74, 86, 86, 86, 86, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 10, 50, 86, 86, 87, 87] 201 rigid atoms, others: [0, 1, 2, 3, 4, 38, 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, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003630 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003630 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003630/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003630 Building REAL300000003631 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003631' /scratch/stefan/7769584/working/building/REAL300000003631 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003631 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003631/0 /scratch/stefan/7769584/working/building/REAL300000003631 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/717 `/scratch/stefan/7769584/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2)C=C1) `REAL300000003631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003631 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 173, 173, 150, 57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 173, 173, 173, 173, 150, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 173, 173] 173 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003631 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [84, 84, 84, 61, 84, 84, 54, 10, 10, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 84, 84, 84, 84, 53, 10, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 84, 84] 173 rigid atoms, others: [37, 9, 10, 11, 12, 13, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003631 none O=C([O-])C1=CC=C(NN=CC2=CN(C3CCOCC3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 40, 40, 84, 84, 84, 174, 174, 174, 174, 174, 84, 84, 1, 1, 1, 1, 11, 40, 84, 174, 174, 174, 174, 174, 174, 174, 174, 174, 84, 1, 1] 174 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 21, 22, 23, 24, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003631 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003631 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003631/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003631 Building REAL300000003632 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003632' /scratch/stefan/7769584/working/building/REAL300000003632 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003632 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003632/0 /scratch/stefan/7769584/working/building/REAL300000003632 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/718 `/scratch/stefan/7769584/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCOCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003632 none CC1=NN(C2CCOCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 199, 199, 199, 199, 199, 81, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 199, 199, 199, 199, 199, 199, 199, 199, 199, 80, 39, 6, 1, 1, 1, 1] 199 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 452 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003632 none CC1=NN(C2CCOCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 62, 62, 178, 199, 199, 178, 199, 199, 199, 199, 199, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 62, 178, 199, 199, 199, 199] 199 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 27, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 573 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003632 none CC1=NN(C2CCOCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 13, 13, 13, 1, 1, 1, 12, 12, 50, 80, 80, 50, 60, 80, 80, 80, 80, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 12, 50, 81, 80, 81, 81] 199 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 36] set([5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003632 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003632 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003632/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003632 Building REAL300000003633 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003633' /scratch/stefan/7769584/working/building/REAL300000003633 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003633 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003633/0 /scratch/stefan/7769584/working/building/REAL300000003633 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/719 `/scratch/stefan/7769584/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2CCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003633 none CC1=NN(C2CCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 170, 170, 170, 170, 94, 40, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 170, 170, 170, 170, 170, 170, 170, 170, 170, 93, 39, 6, 1, 1, 1, 1] 170 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 377 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003633 none CC1=NN(C2CCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 55, 55, 145, 170, 170, 170, 170, 170, 170, 170, 170, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 55, 145, 170, 170, 170, 170] 170 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 414 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: REAL300000003633 none CC1=NN(C2CCCC2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 1, 1, 1, 10, 10, 55, 93, 93, 65, 79, 93, 93, 93, 93, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 10, 55, 93, 93, 94, 94] 170 rigid atoms, others: [0, 1, 2, 3, 4, 9, 10, 11, 35] set([5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 373 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003633 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003633 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003633/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003633 Building REAL300000003634 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003634' /scratch/stefan/7769584/working/building/REAL300000003634 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003634 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003634/0 /scratch/stefan/7769584/working/building/REAL300000003634 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/720 `/scratch/stefan/7769584/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC3=CC=CN=C23)C=C1) `REAL300000003634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003634 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC3=CC=CN=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 19, 6, 1, 1, 1, 1, 1, 22, 22] 22 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26]) 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: REAL300000003634 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC3=CC=CN=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 22, 1, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003634 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003634 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003634/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003634 Building REAL300000003635 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003635' /scratch/stefan/7769584/working/building/REAL300000003635 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003635 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003635/0 /scratch/stefan/7769584/working/building/REAL300000003635 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/721 `/scratch/stefan/7769584/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NN(CC(F)(F)F)C=C2Br)C=C1) `REAL300000003635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003635 none O=C([O-])C1=CC=C(N=NCC2=NN(CC(F)(F)F)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 92, 60, 92, 92, 59, 59, 7, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 1, 92, 92, 92, 92, 7, 7, 9, 9, 1, 92, 92] 201 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) 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: REAL300000003635 none O=C([O-])C1=CC=C(N=NCC2=NN(CC(F)(F)F)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 30, 93, 93, 93, 201, 201, 201, 201, 93, 93, 93, 1, 1, 1, 1, 30, 30, 201, 201, 93, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 686 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003635 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003635/1 /scratch/stefan/7769584/working/building/REAL300000003635 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/722 `/scratch/stefan/7769584/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NN(CC(F)(F)F)C=C2Br)C=C1) `REAL300000003635.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003635 none O=C([O-])C1=CC=C(NN=CC2=NN(CC(F)(F)F)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 89, 126, 74, 126, 126, 74, 12, 12, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 1, 126, 126, 126, 126, 74, 12, 9, 9, 1, 126, 126] 201 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003635 none O=C([O-])C1=CC=C(NN=CC2=NN(CC(F)(F)F)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 45, 45, 127, 127, 127, 201, 201, 201, 201, 127, 127, 127, 1, 1, 1, 1, 11, 45, 201, 201, 127, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003635 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003635 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003635/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003635/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003635 Building REAL300000003636 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003636' /scratch/stefan/7769584/working/building/REAL300000003636 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003636 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003636/0 /scratch/stefan/7769584/working/building/REAL300000003636 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/723 `/scratch/stefan/7769584/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NC3=CC=CC(F)=C3S2)C=C1) `REAL300000003636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003636 none O=C([O-])C1=CC=C(N=NCC2=NC3=CC=CC(F)=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 46, 47, 47, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 8, 8, 1, 1, 1, 47, 47] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003636 none O=C([O-])C1=CC=C(N=NCC2=NC3=CC=CC(F)=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 13, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 13, 13, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003636 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003636 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003636/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003636 Building REAL300000003637 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003637' /scratch/stefan/7769584/working/building/REAL300000003637 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003637 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003637/0 /scratch/stefan/7769584/working/building/REAL300000003637 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/724 `/scratch/stefan/7769584/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003637 none NS(=O)(=O)C1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 45, 88, 88, 45, 44, 45, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 88, 88, 45, 31, 6, 1, 1, 1, 1, 45] 88 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 30]) 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: REAL300000003637 none NS(=O)(=O)C1=CSC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 34, 45, 45, 34, 34, 45, 45, 45, 45, 1, 5, 5, 1, 7, 34, 45, 45, 45, 45, 1] 88 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 23, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003637 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003637 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003637/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003637 Building REAL300000003638 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003638' /scratch/stefan/7769584/working/building/REAL300000003638 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003638 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003638/0 /scratch/stefan/7769584/working/building/REAL300000003638 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/725 `/scratch/stefan/7769584/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C3OC=CC3=CC(Cl)=C2)C=C1) `REAL300000003638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003638 none O=C([O-])C1=CC=C(NN=CC2=C3OC=CC3=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 21, 26, 26, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 21, 7, 1, 1, 1, 1, 26, 26] 26 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000003638 none O=C([O-])C1=CC=C(NN=CC2=C3OC=CC3=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 11, 24, 26, 26, 26, 26, 1, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003638 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003638 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003638/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003638 Building REAL300000003639 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003639' /scratch/stefan/7769584/working/building/REAL300000003639 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003639 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003639/0 /scratch/stefan/7769584/working/building/REAL300000003639 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/726 `/scratch/stefan/7769584/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NC=C(Cl)C=C2Cl)C=C1) `REAL300000003639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003639 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [41, 37, 41, 37, 41, 41, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 37, 9, 1, 1, 41, 41] 42 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) 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: REAL300000003639 none O=C([O-])C1=CC=C(NN=CC2=NC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 8, 25, 42, 42, 1, 1] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003639 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003639/1 /scratch/stefan/7769584/working/building/REAL300000003639 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/727 `/scratch/stefan/7769584/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NC=C(Cl)C=C2Cl)C=C1) `REAL300000003639.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003639 none O=C([O-])C1=CC=C(N=NCC2=NC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 38, 40, 40, 38, 38, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 7, 7, 1, 1, 40, 40] 40 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003639 none O=C([O-])C1=CC=C(N=NCC2=NC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 25, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 25, 25, 40, 40, 1, 1] 40 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003639 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003639 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003639/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003639/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003639 Building REAL300000003640 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003640' /scratch/stefan/7769584/working/building/REAL300000003640 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003640 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003640/0 /scratch/stefan/7769584/working/building/REAL300000003640 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/728 `/scratch/stefan/7769584/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)N=C1C(C)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003640 none CC1=NN(C2=CC=CC=C2)N=C1C(C)N=NC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 4, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 20, 20, 20, 20, 1, 1, 1, 1] 47 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003640 none CC1=NN(C2=CC=CC=C2)N=C1C(C)N=NC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 14, 14, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 1, 1, 1, 1, 1, 14, 14, 14, 14, 47, 47, 47, 47] 47 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, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003640 none CC1=NN(C2=CC=CC=C2)N=C1C(C)N=NC1=CC=C(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', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 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, 3, 3, 2, 3, 3, 1, 1, 1, 10, 10, 46, 46, 47, 47, 46, 46, 47, 47, 47, 47, 2, 2, 2, 3, 3, 2, 3, 3, 10, 10, 10, 10, 47, 47, 47, 47] 47 rigid atoms, others: [0, 1, 2, 3, 4, 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003640 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003640 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003640/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003640 Building REAL300000003641 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003641' /scratch/stefan/7769584/working/building/REAL300000003641 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003641 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003641/0 /scratch/stefan/7769584/working/building/REAL300000003641 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/729 `/scratch/stefan/7769584/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C(Cl)=C2F)C=C1) `REAL300000003641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003641 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 17, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 22, 7, 1, 1, 25, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000003641 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 17, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 10, 24, 25, 25, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003641 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003641 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003641/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003641 Building REAL300000003642 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003642' /scratch/stefan/7769584/working/building/REAL300000003642 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003642 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003642/0 /scratch/stefan/7769584/working/building/REAL300000003642 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/730 `/scratch/stefan/7769584/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003642 none COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 46, 46, 46, 46, 46, 31, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 57, 57, 57, 46, 46, 46, 30, 6, 1, 1, 1, 1] 57 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003642 none COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 38, 46, 46, 38, 38, 46, 46, 46, 46, 1, 1, 3, 3, 3, 1, 1, 1, 10, 38, 46, 46, 46, 46] 57 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25, 26] set([0, 32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003642 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003642 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003642/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003642 Building REAL300000003643 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003643' /scratch/stefan/7769584/working/building/REAL300000003643 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003643 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003643/0 /scratch/stefan/7769584/working/building/REAL300000003643 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/731 `/scratch/stefan/7769584/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(F)=C2F)C=C1) `REAL300000003643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003643 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 16, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 25, 25, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 22, 7, 1, 1, 25, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000003643 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Cl)C(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 16, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 10, 23, 25, 25, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003643 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003643 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003643/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003643 Building REAL300000003644 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003644' /scratch/stefan/7769584/working/building/REAL300000003644 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003644 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003644/0 /scratch/stefan/7769584/working/building/REAL300000003644 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/732 `/scratch/stefan/7769584/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(Cl)=C2F)C=C1) `REAL300000003644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003644 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 15, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 22, 7, 1, 1, 25, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000003644 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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, 1, 15, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 24, 25, 25, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003644 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003644 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003644/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003644 Building REAL300000003645 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003645' /scratch/stefan/7769584/working/building/REAL300000003645 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003645 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003645/0 /scratch/stefan/7769584/working/building/REAL300000003645 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/733 `/scratch/stefan/7769584/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=CC=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=C2)C=N1) `REAL300000003645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003645 none CN1C=C(C2=CC=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 113, 113, 113, 113, 113, 40, 40, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 113, 173, 173, 173, 173, 173, 173, 113, 113, 113, 40, 7, 1, 1, 1, 1, 113, 173] 173 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 282 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003645 none CN1C=C(C2=CC=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 64, 113, 113, 73, 113, 113, 113, 113, 113, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 13, 64, 113, 113, 113, 113, 1, 5] 173 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 28, 29, 30, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003645 none CN1C=C(C2=CC=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 5, 5, 35, 35, 146, 173, 173, 173, 173, 173, 173, 173, 173, 5, 1, 1, 2, 2, 2, 1, 5, 5, 5, 35, 146, 173, 173, 173, 173, 5, 1] 173 rigid atoms, others: [0, 1, 2, 3, 4, 38, 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, 35, 36, 37]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003645 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003645 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003645/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003645 Building REAL300000003646 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003646' /scratch/stefan/7769584/working/building/REAL300000003646 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003646 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003646/0 /scratch/stefan/7769584/working/building/REAL300000003646 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/734 `/scratch/stefan/7769584/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br) `REAL300000003646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003646 none COC1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 35, 52, 52, 52, 29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 52, 52, 52, 52, 52, 52, 52, 29, 7, 1, 1, 1, 1, 52] 52 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003646 none COC1=CC(F)=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 52, 52, 47, 52, 52, 52, 52, 52, 1, 1, 1, 4, 4, 4, 1, 9, 41, 52, 52, 52, 52, 1] 52 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003646 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003646 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003646/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003646 Building REAL300000003647 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003647' /scratch/stefan/7769584/working/building/REAL300000003647 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003647 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003647/0 /scratch/stefan/7769584/working/building/REAL300000003647 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/735 `/scratch/stefan/7769584/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C([N+](=O)[O-])C(OC3CC3)=C2)C=C1) `REAL300000003647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003647 none O=C([O-])C1=CC=C(NN=CC2=CC=C([N+](=O)[O-])C(OC3CC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 189, 99, 99, 27, 27, 27, 27, 27, 27, 27, 27, 10, 1, 1, 1, 1, 27, 201, 201, 201, 201, 189, 99, 27, 27, 1, 1, 1, 1, 1, 27, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 512 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003647 none O=C([O-])C1=CC=C(NN=CC2=CC=C([N+](=O)[O-])C(OC3CC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 89, 137, 137, 77, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 1, 137, 137, 137, 137, 77, 11, 1, 1, 27, 27, 27, 27, 27, 1, 137, 138] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 523 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003647 none O=C([O-])C1=CC=C(NN=CC2=CC=C([N+](=O)[O-])C(OC3CC3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 42, 43, 142, 142, 142, 142, 142, 142, 142, 142, 189, 201, 201, 142, 1, 1, 1, 1, 11, 42, 142, 142, 201, 201, 201, 201, 201, 141, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 343 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003647 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003647 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003647/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003647 Building REAL300000003648 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003648' /scratch/stefan/7769584/working/building/REAL300000003648 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003648 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003648/0 /scratch/stefan/7769584/working/building/REAL300000003648 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/736 `/scratch/stefan/7769584/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003648 none CC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 40, 24, 7, 1, 1, 1, 1] 40 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 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: REAL300000003648 none CC1=CC=C(Br)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 36, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 1, 12, 36, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/7769584/working/building/REAL300000003648 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003648 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003648/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003648 Building REAL300000003649 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003649' /scratch/stefan/7769584/working/building/REAL300000003649 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003649 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003649/0 /scratch/stefan/7769584/working/building/REAL300000003649 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/737 `/scratch/stefan/7769584/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2S1) `REAL300000003649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003649 none COC1=NC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 26, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 61, 61, 61, 61, 61, 61, 61, 25, 6, 1, 1, 1, 1, 60] 61 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003649 none COC1=NC2=CC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 60, 60, 40, 52, 60, 61, 61, 60, 1, 1, 1, 7, 7, 7, 1, 1, 10, 40, 60, 60, 61, 61, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 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/7769584/working/building/REAL300000003649 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003649 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003649/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003649 Building REAL300000003650 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003650' /scratch/stefan/7769584/working/building/REAL300000003650 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003650 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003650/0 /scratch/stefan/7769584/working/building/REAL300000003650 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/738 `/scratch/stefan/7769584/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=NC(Br)=C2)C=C1) `REAL300000003650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003650 none O=C([O-])C1=CC=C(NN=CC2=CC=NC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 28, 6, 1, 1, 1, 34, 34] 35 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 26, 27]) 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: REAL300000003650 none O=C([O-])C1=CC=C(NN=CC2=CC=NC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 9, 20, 35, 35, 35, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003650 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003650 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003650/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003650 Building REAL300000003651 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003651' /scratch/stefan/7769584/working/building/REAL300000003651 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003651 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003651/0 /scratch/stefan/7769584/working/building/REAL300000003651 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/739 `/scratch/stefan/7769584/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC(Cl)=C2Cl)C=C1) `REAL300000003651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003651 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', '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, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 30, 26, 30, 30, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 26, 10, 1, 1, 30, 30] 30 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003651 none O=C([O-])C1=CC=C(NN=CC2=CC(F)=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', '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, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 9, 24, 30, 30, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003651 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003651 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003651/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003651 Building REAL300000003652 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003652' /scratch/stefan/7769584/working/building/REAL300000003652 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003652 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003652/0 /scratch/stefan/7769584/working/building/REAL300000003652 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/740 `/scratch/stefan/7769584/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003652 none CC(C)(C)COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 94, 94, 94, 94, 94, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 37, 6, 1, 1, 1, 1, 94] 201 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 409 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: REAL300000003652 none CC(C)(C)COC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 56, 94, 94, 59, 62, 94, 94, 94, 94, 1, 23, 23, 23, 22, 22, 22, 23, 23, 23, 19, 19, 1, 1, 1, 11, 56, 94, 94, 94, 94, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 44, 23, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 462 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003652 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003652 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003652/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003652 Building REAL300000003653 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003653' /scratch/stefan/7769584/working/building/REAL300000003653 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003653 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003653/0 /scratch/stefan/7769584/working/building/REAL300000003653 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/741 `/scratch/stefan/7769584/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(Cl)=C2F)C=C1) `REAL300000003653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003653 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 23, 27, 27, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 28, 23, 6, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003653 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(Cl)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 16, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 23, 28, 28, 1, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003653 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003653 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003653/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003653 Building REAL300000003654 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003654' /scratch/stefan/7769584/working/building/REAL300000003654 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003654 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003654/0 /scratch/stefan/7769584/working/building/REAL300000003654 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/742 `/scratch/stefan/7769584/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003654 none COC1=CC(Cl)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 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', '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, 12, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 48, 48, 48, 48, 48, 48, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 70, 70, 70, 48, 48, 28, 6, 1, 1, 1, 1, 47] 70 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003654 none COC1=CC(Cl)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 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', '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, 12, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 47, 47, 36, 36, 47, 47, 47, 47, 1, 3, 3, 3, 1, 1, 8, 36, 47, 48, 47, 47, 1] 70 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 20, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003654 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003654 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003654/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003654 Building REAL300000003655 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003655' /scratch/stefan/7769584/working/building/REAL300000003655 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003655 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003655/0 /scratch/stefan/7769584/working/building/REAL300000003655 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/743 `/scratch/stefan/7769584/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(C(F)(F)F)=C2Cl)C=C1) `REAL300000003655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003655 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(C(F)(F)F)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', '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, 1, 15, 1, 5, 15, 15, 15, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 27, 21, 27, 27, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 27, 27, 27, 27, 21, 10, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31]) 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: REAL300000003655 none O=C([O-])C1=CC=C(NN=CC2=CC=C(F)C(C(F)(F)F)=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', '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, 1, 15, 1, 5, 15, 15, 15, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 21, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 21, 27, 27, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003655 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003655 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003655/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003655 Building REAL300000003656 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003656' /scratch/stefan/7769584/working/building/REAL300000003656 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003656 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003656/0 /scratch/stefan/7769584/working/building/REAL300000003656 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/744 `/scratch/stefan/7769584/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(F)=C1F) `REAL300000003656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003656 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 39, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81, 39, 6, 1, 1, 1, 1, 81] 81 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003656 none COC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(F)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 13, 13, 58, 81, 81, 58, 58, 81, 81, 81, 81, 1, 1, 1, 1, 1, 4, 4, 4, 1, 13, 58, 81, 81, 81, 81, 1] 81 rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003656 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003656 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003656/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003656 Building REAL300000003657 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003657' /scratch/stefan/7769584/working/building/REAL300000003657 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003657 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003657/0 /scratch/stefan/7769584/working/building/REAL300000003657 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/745 `/scratch/stefan/7769584/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003657 none CC1=CC(Br)=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 22, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 21, 6, 1, 1, 1, 1, 25] 25 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003657 none CC1=CC(Br)=C(F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 1, 7, 20, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 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/7769584/working/building/REAL300000003657 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003657 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003657/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003657 Building REAL300000003658 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003658' /scratch/stefan/7769584/working/building/REAL300000003658 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003658 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003658/0 /scratch/stefan/7769584/working/building/REAL300000003658 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/746 `/scratch/stefan/7769584/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCC3=C2C=CC(Br)=C3F)C=C1) `REAL300000003658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003658 none O=C([O-])C1=CC=C(NN=C2CCC3=C2C=CC(Br)=C3F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 6, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 9, 9] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24, 31]) total number of confs: 35 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: REAL300000003658 none O=C([O-])C1=CC=C(NN=C2CCC3=C2C=CC(Br)=C3F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 17, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 1, 1] 9 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 21 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003658 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003658 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003658/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003658 Building REAL300000003659 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003659' /scratch/stefan/7769584/working/building/REAL300000003659 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003659 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003659/0 /scratch/stefan/7769584/working/building/REAL300000003659 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/747 `/scratch/stefan/7769584/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC(Br)=CC=C21) `REAL300000003659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003659 none CC1CC(=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC(Br)=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 12, 12, 12] 12 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 24 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: REAL300000003659 none CC1CC(=NNC2=CC=C(C(=O)[O-])C=C2)C2=CC(Br)=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 12, 12, 6, 6, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 6, 12, 12, 12, 12, 1, 1, 1] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 33, 34, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003659 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003659 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003659/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003659 Building REAL300000003660 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003660' /scratch/stefan/7769584/working/building/REAL300000003660 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003660 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003660/0 /scratch/stefan/7769584/working/building/REAL300000003660 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/748 `/scratch/stefan/7769584/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2SC(CN=NC3=CC=C(C(=O)[O-])C=C3)=NC2=C1) `REAL300000003660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003660 none COC1=CC=C2SC(CN=NC3=CC=C(C(=O)[O-])C=C3)=NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 89, 89, 89, 89, 89, 89, 19, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 89, 89, 89, 94, 94, 94, 89, 89, 19, 19, 1, 1, 1, 1, 89] 94 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003660 none COC1=CC=C2SC(CN=NC3=CC=C(C(=O)[O-])C=C3)=NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 74, 75, 89, 89, 75, 75, 89, 89, 89, 89, 1, 1, 1, 3, 3, 3, 1, 1, 8, 8, 89, 89, 89, 89, 1] 94 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 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/7769584/working/building/REAL300000003660 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003660 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003660/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003660 Building REAL300000003661 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003661' /scratch/stefan/7769584/working/building/REAL300000003661 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003661 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003661/0 /scratch/stefan/7769584/working/building/REAL300000003661 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/749 `/scratch/stefan/7769584/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=CN=C3)N2)C=C1) `REAL300000003661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003661 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=CN=C3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 187, 201, 187, 201, 201, 187, 53, 53, 37, 37, 37, 37, 8, 1, 1, 1, 1, 1, 1, 37, 201, 201, 201, 201, 187, 53, 37, 37, 8, 8, 1, 1, 1, 37, 201, 201] 201 rigid atoms, others: [32, 33, 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, 34, 35, 36]) total number of confs: 604 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003661 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=CN=C3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 19, 39, 19, 39, 39, 19, 5, 5, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 1, 39, 39, 39, 39, 19, 5, 1, 1, 9, 9, 37, 37, 37, 1, 39, 39] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 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: REAL300000003661 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=CN=C3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 33, 33, 41, 41, 41, 41, 117, 201, 201, 201, 201, 41, 1, 1, 1, 1, 8, 33, 41, 41, 117, 117, 201, 201, 201, 41, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003661 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003661 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003661/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003661 Building REAL300000003662 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003662' /scratch/stefan/7769584/working/building/REAL300000003662 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003662 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003662/0 /scratch/stefan/7769584/working/building/REAL300000003662 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/750 `/scratch/stefan/7769584/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)CCCC2=N1) `REAL300000003662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003662 none N#CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)CCCC2=N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10] 10 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 22 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: REAL300000003662 none N#CC1=CC=C2C(=NNC3=CC=C(C(=O)[O-])C=C3)CCCC2=N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 5, 5, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29]) total number of confs: 46 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003662 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003662 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003662/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003662 Building REAL300000003663 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003663' /scratch/stefan/7769584/working/building/REAL300000003663 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003663 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003663/0 /scratch/stefan/7769584/working/building/REAL300000003663 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/751 `/scratch/stefan/7769584/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC([N+](=O)[O-])=CC(Br)=C1[O-]) `REAL300000003663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003663 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC([N+](=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 15, 21, 21, 15, 19, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003663 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC([N+](=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 6, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003663 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003663 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003663/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003663 Building REAL300000003664 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003664' /scratch/stefan/7769584/working/building/REAL300000003664 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003664 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003664/0 /scratch/stefan/7769584/working/building/REAL300000003664 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/752 `/scratch/stefan/7769584/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(Br)=CC=C23)C=C1) `REAL300000003664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003664 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(Br)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [46, 33, 46, 33, 46, 46, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 33, 8, 1, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 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: REAL300000003664 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(Br)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 9, 37, 47, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003664 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003664/1 /scratch/stefan/7769584/working/building/REAL300000003664 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/753 `/scratch/stefan/7769584/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(Br)=CC=C23)C=C1) `REAL300000003664.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003664 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(Br)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 9, 9, 1, 1, 1, 1, 1, 44, 44] 44 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003664 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(Br)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 15, 15, 44, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003664 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003664 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003664/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003664/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003664 Building REAL300000003665 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003665' /scratch/stefan/7769584/working/building/REAL300000003665 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003665 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003665/0 /scratch/stefan/7769584/working/building/REAL300000003665 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/754 `/scratch/stefan/7769584/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N2N=CC(C#N)=C12) `REAL300000003665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003665 none CN1C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N2N=CC(C#N)=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 8, 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, 2, 2, 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, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 1, 1, 1, 1, 43] 43 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003665 none CN1C=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N2N=CC(C#N)=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 43, 43, 43, 43, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003665 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003665/1 /scratch/stefan/7769584/working/building/REAL300000003665 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/755 `/scratch/stefan/7769584/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N2N=CC(C#N)=C12) `REAL300000003665.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003665 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N2N=CC(C#N)=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', '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, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 19, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 6, 1, 1, 1, 1, 28] 28 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003665 none CN1C=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N2N=CC(C#N)=C12 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', '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, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 24, 28, 28, 24, 24, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 24, 28, 28, 28, 28, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 33, 16, 17, 18, 19, 20, 21, 22, 26] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003665 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003665 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003665/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003665/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003665 Building REAL300000003666 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003666' /scratch/stefan/7769584/working/building/REAL300000003666 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003666 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003666/0 /scratch/stefan/7769584/working/building/REAL300000003666 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/756 `/scratch/stefan/7769584/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1C1=NNC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003666 none CN1N=CC=C1C1=NNC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 156, 100, 100, 100, 100, 100, 34, 34, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 156, 156, 156, 156, 156, 100, 100, 34, 7, 1, 1, 1, 1] 156 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 238 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003666 none CN1N=CC=C1C1=NNC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 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: [10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 68, 100, 100, 68, 91, 100, 100, 100, 100, 10, 10, 10, 10, 10, 1, 1, 13, 68, 100, 100, 100, 100] 156 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 367 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003666 none CN1N=CC=C1C1=NNC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 52, 52, 126, 156, 156, 126, 156, 156, 156, 156, 156, 2, 2, 2, 1, 1, 10, 10, 52, 126, 156, 156, 156, 156] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 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, 35]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003666 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003666 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003666/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003666 Building REAL300000003667 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003667' /scratch/stefan/7769584/working/building/REAL300000003667 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003667 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003667/0 /scratch/stefan/7769584/working/building/REAL300000003667 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/757 `/scratch/stefan/7769584/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN=C3C=C(Br)C=CN23)C=C1) `REAL300000003667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003667 none O=C([O-])C1=CC=C(NN=CC2=CN=C3C=C(Br)C=CN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 38, 48, 48, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 38, 11, 1, 1, 1, 1, 48, 48] 48 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000003667 none O=C([O-])C1=CC=C(NN=CC2=CN=C3C=C(Br)C=CN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 29, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 9, 29, 47, 47, 47, 47, 1, 1] 48 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003667 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003667 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003667/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003667 Building REAL300000003668 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003668' /scratch/stefan/7769584/working/building/REAL300000003668 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003668 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003668/0 /scratch/stefan/7769584/working/building/REAL300000003668 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/758 `/scratch/stefan/7769584/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1) `REAL300000003668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003668 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 39, 39, 125, 138, 138, 125, 138, 138, 138, 138, 138, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 5, 5, 5, 39, 125, 138, 138, 138, 138, 1, 1, 1, 1] 138 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003668 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 98, 98, 98, 138, 138, 98, 138, 138, 138, 138, 138, 138, 98, 98, 98, 98, 33, 7, 1, 1, 1, 1, 138, 138, 98, 138] 138 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 13, 14] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003668 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 13, 13, 80, 98, 98, 80, 95, 98, 98, 98, 98, 1, 1, 1, 4, 4, 1, 4, 4, 5, 5, 5, 4, 1, 2, 2, 2, 13, 80, 98, 98, 98, 98, 4, 4, 1, 4] 138 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003668 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003668/1 /scratch/stefan/7769584/working/building/REAL300000003668 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/759 `/scratch/stefan/7769584/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1) `REAL300000003668.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003668 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 29, 105, 105, 113, 113, 105, 105, 113, 113, 113, 113, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 5, 5, 5, 29, 29, 113, 113, 113, 113, 1, 1, 1, 1] 113 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 280 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003668 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 29, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 113, 113, 113, 113, 113, 113, 113, 113, 113, 76, 76, 76, 76, 29, 29, 1, 1, 1, 1, 113, 113, 113, 113] 113 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003668 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 52, 52, 76, 76, 52, 52, 76, 76, 76, 76, 1, 1, 1, 4, 4, 2, 4, 4, 5, 5, 5, 4, 1, 2, 2, 2, 8, 8, 76, 76, 76, 76, 4, 4, 2, 4] 113 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003668 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003668 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003668/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003668/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003668 Building REAL300000003669 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003669' /scratch/stefan/7769584/working/building/REAL300000003669 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003669 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003669/0 /scratch/stefan/7769584/working/building/REAL300000003669 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/760 `/scratch/stefan/7769584/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C) `REAL300000003669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003669 none COC(=O)C1=C(C)NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 45, 66, 45, 45, 45, 45, 34, 34, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 45, 66, 66, 66, 45, 45, 45, 45, 34, 7, 1, 1, 1, 1, 45, 45, 45] 66 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003669 none COC(=O)C1=C(C)NC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 8, 8, 31, 45, 45, 31, 31, 45, 45, 45, 45, 1, 1, 13, 13, 13, 2, 2, 2, 1, 8, 31, 45, 45, 45, 45, 2, 2, 2] 66 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 22, 29] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003669 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003669 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003669/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003669 Building REAL300000003670 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003670' /scratch/stefan/7769584/working/building/REAL300000003670 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003670 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003670/0 /scratch/stefan/7769584/working/building/REAL300000003670 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/761 `/scratch/stefan/7769584/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C2C1) `REAL300000003670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003670 none CC(C)(C)OC(=O)N1CCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C2C1 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 144, 95, 144, 95, 95, 95, 95, 95, 36, 36, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 95, 95, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 95, 95, 36, 7, 1, 1, 1, 1, 95, 95, 95, 95] 201 rigid atoms, others: [48, 45, 46, 15, 16, 17, 18, 19, 20, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52]) 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: REAL300000003670 none CC(C)(C)OC(=O)N1CCC2=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=CC=C2C1 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 52, 95, 95, 52, 52, 95, 95, 95, 95, 1, 1, 1, 1, 23, 23, 23, 22, 22, 22, 23, 23, 23, 1, 1, 1, 1, 1, 11, 52, 95, 95, 95, 95, 1, 1, 1, 1] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 49, 40, 50, 51, 52, 41, 25, 26, 27, 28, 42] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003670 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003670 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003670/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003670 Building REAL300000003671 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003671' /scratch/stefan/7769584/working/building/REAL300000003671 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003671 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003671/0 /scratch/stefan/7769584/working/building/REAL300000003671 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/762 `/scratch/stefan/7769584/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003671 none CC1=CC(Br)=CC(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 20, 20, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 20, 7, 1, 1, 1, 1] 28 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003671 none CC1=CC(Br)=CC(C)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 28, 28, 24, 24, 28, 28, 28, 28, 2, 2, 2, 1, 1, 2, 2, 2, 6, 24, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003671 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003671 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003671/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003671 Building REAL300000003672 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003672' /scratch/stefan/7769584/working/building/REAL300000003672 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003672 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003672/0 /scratch/stefan/7769584/working/building/REAL300000003672 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/763 `/scratch/stefan/7769584/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC(F)=C2Br)C=C1) `REAL300000003672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003672 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC(F)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 15, 1, 17, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 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: [52, 52, 52, 40, 52, 52, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 40, 12, 2, 1, 1, 52, 52] 104 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 28, 29]) 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: REAL300000003672 none O=C([O-])C1=CC=C(NN=CC2=C(O)C=CC(F)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 15, 1, 17, 1, 1, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 9, 31, 104, 52, 52, 1, 1] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003672 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003672/1 /scratch/stefan/7769584/working/building/REAL300000003672 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/764 `/scratch/stefan/7769584/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C([O-])C=CC(F)=C2Br)C=C1) `REAL300000003672.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003672 none O=C([O-])C1=CC=C(NN=CC2=C([O-])C=CC(F)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 15, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 17, 13, 17, 17, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 13, 5, 1, 1, 17, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000003672 none O=C([O-])C1=CC=C(NN=CC2=C([O-])C=CC(F)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 15, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 11, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003672 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003672 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003672/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003672/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003672 Building REAL300000003673 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003673' /scratch/stefan/7769584/working/building/REAL300000003673 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003673 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003673/0 /scratch/stefan/7769584/working/building/REAL300000003673 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/765 `/scratch/stefan/7769584/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2O)C=C1) `REAL300000003673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003673 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [23, 18, 23, 18, 23, 23, 18, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 23, 23, 23, 23, 18, 6, 1, 1, 1, 2, 23, 23] 46 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 15, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 96 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: REAL300000003673 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 10, 21, 23, 23, 23, 46, 1, 1] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003673 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003673 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003673/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003673 Building REAL300000003674 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003674' /scratch/stefan/7769584/working/building/REAL300000003674 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003674 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003674/0 /scratch/stefan/7769584/working/building/REAL300000003674 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/766 `/scratch/stefan/7769584/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1) `REAL300000003674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003674 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 27, 27, 53, 65, 65, 53, 53, 65, 65, 65, 65, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 27, 52, 65, 65, 65, 65, 1, 1, 1, 1, 1] 65 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]) total number of confs: 230 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003674 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 28, 6, 1, 1, 1, 1, 64, 65, 65, 65, 65] 65 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003674 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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 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, 13, 13, 53, 65, 65, 53, 53, 65, 65, 65, 65, 1, 1, 1, 3, 3, 1, 3, 3, 1, 2, 2, 2, 13, 53, 65, 65, 65, 65, 4, 4, 1, 4, 4] 65 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003674 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003674/1 /scratch/stefan/7769584/working/building/REAL300000003674 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/767 `/scratch/stefan/7769584/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1) `REAL300000003674.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003674 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 46, 46, 46, 46, 1, 1, 1, 1, 1] 46 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003674 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 21, 21, 1, 1, 1, 1, 46, 46, 46, 46, 46] 46 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) 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: REAL300000003674 none CC1=C(CN=NC2=CC=C(C(=O)[O-])C=C2)N=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 40, 40, 46, 46, 44, 44, 46, 46, 46, 46, 1, 1, 1, 4, 4, 1, 4, 4, 1, 2, 2, 2, 7, 7, 46, 46, 46, 46, 4, 4, 1, 4, 4] 46 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003674 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003674 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003674/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003674/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003674 Building REAL300000003675 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003675' /scratch/stefan/7769584/working/building/REAL300000003675 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003675 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003675/0 /scratch/stefan/7769584/working/building/REAL300000003675 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/768 `/scratch/stefan/7769584/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl) `REAL300000003675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003675 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 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, 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, 154, 74, 70, 74, 74, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 201, 201, 74, 73, 23, 5, 1, 1, 1, 1, 74] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003675 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 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, 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: [70, 38, 70, 9, 1, 1, 1, 1, 1, 1, 6, 6, 40, 73, 73, 40, 40, 73, 73, 73, 73, 1, 1, 1, 38, 38, 1, 1, 6, 40, 74, 74, 73, 73, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003675 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003675 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003675/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003675 Building REAL300000003676 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003676' /scratch/stefan/7769584/working/building/REAL300000003676 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003676 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003676/0 /scratch/stefan/7769584/working/building/REAL300000003676 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/769 `/scratch/stefan/7769584/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003676 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 29, 12, 29, 29, 12, 29, 29, 12, 12, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 29, 49, 49, 43, 29, 29, 12, 4, 1, 1, 1, 1, 29, 29] 49 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003676 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 21, 29, 29, 23, 29, 29, 29, 29, 29, 1, 1, 9, 9, 5, 1, 1, 7, 21, 29, 29, 29, 29, 1, 1] 49 rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003676 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003676 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003676/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003676 Building REAL300000003677 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003677' /scratch/stefan/7769584/working/building/REAL300000003677 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003677 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003677/0 /scratch/stefan/7769584/working/building/REAL300000003677 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/770 `/scratch/stefan/7769584/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C)C=C1Br) `REAL300000003677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003677 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 20, 38, 38, 20, 20, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 38, 38, 38, 38, 1, 1, 2, 2, 2, 1] 38 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 191 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003677 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 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: [24, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 38, 38, 38, 38, 38, 38, 38, 25, 25, 25, 5, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003677 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003677 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003677/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003677 Building REAL300000003678 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003678' /scratch/stefan/7769584/working/building/REAL300000003678 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003678 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003678/0 /scratch/stefan/7769584/working/building/REAL300000003678 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/771 `/scratch/stefan/7769584/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Br)=C2)C=C1) `REAL300000003678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003678 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 142, 85, 142, 142, 85, 12, 12, 1, 12, 58, 91, 91, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 85, 58, 58, 91, 91, 91, 91, 91, 1, 1, 1, 1, 142, 142] 201 rigid atoms, others: [33, 34, 35, 36, 9, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 902 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003678 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 117, 73, 117, 117, 72, 17, 17, 3, 1, 1, 1, 1, 17, 91, 91, 91, 91, 91, 91, 117, 117, 117, 117, 72, 3, 3, 1, 1, 1, 1, 1, 91, 91, 91, 91, 117, 117] 201 rigid atoms, others: [32, 10, 11, 12, 13, 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, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 595 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: REAL300000003678 none O=C([O-])C1=CC=C(NN=C(CC2CC2)C2=CC=CC(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 30, 30, 91, 116, 116, 30, 148, 148, 148, 148, 148, 148, 1, 1, 1, 1, 9, 91, 91, 116, 116, 116, 116, 116, 148, 148, 148, 148, 1, 1] 200 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 545 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003678 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003678 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003678/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003678 Building REAL300000003679 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003679' /scratch/stefan/7769584/working/building/REAL300000003679 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003679 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003679/0 /scratch/stefan/7769584/working/building/REAL300000003679 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/772 `/scratch/stefan/7769584/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003679 none CC1=NOC(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 100, 100, 100, 100, 100, 100, 36, 36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 100, 100, 100, 100, 36, 7, 1, 1, 1, 1, 133] 133 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003679 none CC1=NOC(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 58, 100, 100, 58, 58, 100, 100, 100, 100, 12, 12, 12, 12, 1, 1, 1, 1, 10, 58, 100, 100, 100, 100, 12] 133 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 465 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003679 none CC1=NOC(C2=CC=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 11, 12, 12, 12, 40, 40, 110, 133, 133, 110, 110, 133, 133, 133, 133, 1, 2, 2, 2, 12, 12, 12, 12, 40, 110, 133, 133, 133, 133, 1] 133 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 37] 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]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003679 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003679 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003679/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003679 Building REAL300000003680 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003680' /scratch/stefan/7769584/working/building/REAL300000003680 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003680 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003680/0 /scratch/stefan/7769584/working/building/REAL300000003680 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/773 `/scratch/stefan/7769584/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Br)N=C(C(F)F)S2)C=C1) `REAL300000003680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003680 none O=C([O-])C1=CC=C(NN=CC2=C(Br)N=C(C(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 1, 5, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [103, 69, 103, 69, 103, 103, 69, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 103, 103, 103, 103, 68, 12, 12, 103, 103] 124 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003680 none O=C([O-])C1=CC=C(NN=CC2=C(Br)N=C(C(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 1, 5, 15, 15, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 9, 38, 38, 78, 78, 78, 78, 78, 91, 91, 78, 1, 1, 1, 1, 9, 38, 91, 1, 1] 91 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003680 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003680 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003680/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003680 Building REAL300000003681 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003681' /scratch/stefan/7769584/working/building/REAL300000003681 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003681 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003681/0 /scratch/stefan/7769584/working/building/REAL300000003681 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/774 `/scratch/stefan/7769584/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(O)=C([O-])C([N+](=O)[O-])=C2)C=C1) `REAL300000003681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003681 none O=C([O-])C1=CC=C(NN=CC2=CC(O)=C([O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 12, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [41, 33, 41, 33, 41, 41, 33, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 33, 12, 1, 2, 1, 42, 42] 84 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 27, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 21, 22, 23, 24, 25, 26, 28, 30, 31]) 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: REAL300000003681 none O=C([O-])C1=CC=C(NN=CC2=CC(O)=C([O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 12, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 7, 28, 42, 84, 41, 1, 1] 84 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003681 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003681 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003681/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003681 Building REAL300000003682 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003682' /scratch/stefan/7769584/working/building/REAL300000003682 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003682 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003682/0 /scratch/stefan/7769584/working/building/REAL300000003682 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/775 `/scratch/stefan/7769584/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CSC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003682 none NS(=O)(=O)C1=CSC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 67, 73, 73, 67, 67, 67, 67, 29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 73, 67, 67, 29, 7, 1, 1, 1, 1] 73 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26]) 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: REAL300000003682 none NS(=O)(=O)C1=CSC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 46, 67, 67, 61, 67, 67, 67, 67, 67, 5, 5, 1, 1, 10, 46, 67, 67, 67, 67] 73 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 23, 24] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003682 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003682 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003682/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003682 Building REAL300000003683 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003683' /scratch/stefan/7769584/working/building/REAL300000003683 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003683 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003683/0 /scratch/stefan/7769584/working/building/REAL300000003683 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/776 `/scratch/stefan/7769584/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1) `REAL300000003683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003683 none CN1N=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 2, 2, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 19, 19, 34, 39, 39, 39, 39, 39, 39, 39, 39, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 19, 34, 39, 39, 39, 39, 12, 1, 1, 1] 39 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: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003683 none CN1N=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 2, 2, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 22, 22, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 31, 31, 39, 39, 39, 39, 31, 31, 31, 22, 7, 1, 1, 1, 1, 31, 39, 39, 39] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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: REAL300000003683 none CN1N=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 2, 2, 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 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, 6, 6, 23, 31, 31, 29, 31, 31, 31, 31, 31, 1, 1, 1, 12, 12, 12, 12, 2, 2, 2, 6, 23, 31, 31, 31, 31, 1, 12, 12, 12] 39 rigid atoms, others: [0, 1, 2, 3, 4, 32, 16, 17, 18] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003683 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003683/1 /scratch/stefan/7769584/working/building/REAL300000003683 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/777 `/scratch/stefan/7769584/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1) `REAL300000003683.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003683 none CN1N=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 49, 137, 137, 139, 139, 137, 137, 139, 139, 139, 139, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 49, 49, 139, 139, 139, 139, 13, 1, 1, 1] 139 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: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003683 none CN1N=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 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: [91, 91, 91, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 139, 139, 139, 139, 91, 91, 91, 21, 21, 1, 1, 1, 1, 91, 139, 139, 139] 139 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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: REAL300000003683 none CN1N=C(CN=NC2=CC=C(C(=O)[O-])C=C2)C=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 59, 59, 91, 91, 59, 59, 91, 91, 91, 91, 1, 1, 1, 13, 13, 13, 13, 2, 2, 2, 9, 9, 91, 91, 91, 91, 1, 13, 13, 13] 139 rigid atoms, others: [0, 1, 2, 3, 4, 32, 16, 17, 18] 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]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003683 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003683 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003683/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003683/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003683 Building REAL300000003684 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003684' /scratch/stefan/7769584/working/building/REAL300000003684 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003684 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003684/0 /scratch/stefan/7769584/working/building/REAL300000003684 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/778 `/scratch/stefan/7769584/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC3=C2OCO3)C=C1) `REAL300000003684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003684 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 35, 40, 40, 34, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 34, 11, 1, 1, 1, 1, 40, 40] 40 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003684 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C=CC3=C2OCO3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 9, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 9, 24, 40, 40, 40, 40, 1, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003684 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003684 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003684/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003684 Building REAL300000003685 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003685' /scratch/stefan/7769584/working/building/REAL300000003685 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003685 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003685/0 /scratch/stefan/7769584/working/building/REAL300000003685 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/779 `/scratch/stefan/7769584/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CCCCC3)C=C2)C=C1) `REAL300000003685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003685 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CCCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 49, 17, 17, 2, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 61, 61, 61, 61, 49, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 61, 61] 61 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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, 41, 42, 43, 44]) total number of confs: 164 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003685 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CCCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 28, 28, 22, 7, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 28, 28, 28, 28, 22, 7, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 28, 28] 61 rigid atoms, others: [9, 10, 11, 12, 13, 14, 42, 20, 21, 41, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) 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: REAL300000003685 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3CCCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 23, 23, 28, 28, 23, 25, 61, 61, 61, 61, 61, 28, 28, 1, 1, 1, 1, 9, 23, 28, 28, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 28, 28, 1, 1] 61 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003685 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003685 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003685/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003685 Building REAL300000003686 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003686' /scratch/stefan/7769584/working/building/REAL300000003686 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003686 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003686/0 /scratch/stefan/7769584/working/building/REAL300000003686 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/780 `/scratch/stefan/7769584/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(Br)=C1) `REAL300000003686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003686 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(Br)=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 45, 46, 46, 46, 46, 46, 28, 6, 1, 1, 1, 1, 46] 46 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003686 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(Br)=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 40, 46, 46, 40, 40, 46, 46, 46, 46, 1, 1, 1, 1, 2, 2, 2, 12, 40, 46, 46, 46, 46, 1] 46 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003686 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003686 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003686/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003686 Building REAL300000003687 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003687' /scratch/stefan/7769584/working/building/REAL300000003687 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003687 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003687/0 /scratch/stefan/7769584/working/building/REAL300000003687 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/781 `/scratch/stefan/7769584/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=NN1CC(F)F) `REAL300000003687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003687 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=NN1CC(F)F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 32, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 193, 201, 201, 108, 108, 108, 31, 6, 1, 1, 1, 1, 108, 193, 193, 201] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003687 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=NN1CC(F)F 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 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, 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, 10, 10, 72, 108, 108, 72, 74, 108, 108, 108, 108, 1, 1, 1, 1, 5, 27, 27, 2, 2, 2, 10, 72, 108, 108, 108, 108, 1, 5, 5, 27] 201 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003687 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003687 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003687/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003687 Building REAL300000003688 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003688' /scratch/stefan/7769584/working/building/REAL300000003688 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003688 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003688/0 /scratch/stefan/7769584/working/building/REAL300000003688 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/782 `/scratch/stefan/7769584/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2CCCC(N=NC3=CC=C(C(=O)[O-])C=C3)CC2=C1) `REAL300000003688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003688 none COC1=CC=C2CCCC(N=NC3=CC=C(C(=O)[O-])C=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', '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, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12] 12 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003688 none COC1=CC=C2CCCC(N=NC3=CC=C(C(=O)[O-])C=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', '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, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 12, 10, 10, 12, 11, 12, 12, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 1] 12 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42] set([0, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003688 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003688 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003688/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003688 Building REAL300000003689 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003689' /scratch/stefan/7769584/working/building/REAL300000003689 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003689 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003689/0 /scratch/stefan/7769584/working/building/REAL300000003689 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/783 `/scratch/stefan/7769584/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC3(C2)CCC(F)(F)CC3)C=C1) `REAL300000003689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003689 none O=C([O-])C1=CC=C(N=NC2CC3(C2)CCC(F)(F)CC3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 38, 37]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003689 none O=C([O-])C1=CC=C(N=NC2CC3(C2)CCC(F)(F)CC3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003689 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003689 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003689/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003689 Building REAL300000003690 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003690' /scratch/stefan/7769584/working/building/REAL300000003690 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003690 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003690/0 /scratch/stefan/7769584/working/building/REAL300000003690 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/784 `/scratch/stefan/7769584/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=N3)N=C2)C=C1) `REAL300000003690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003690 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=N3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 40, 45, 45, 39, 13, 13, 3, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 45, 45, 45, 45, 39, 13, 4, 4, 1, 1, 1, 1, 4, 45, 45] 45 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, 36]) total number of confs: 135 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003690 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=N3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 43, 45, 36, 45, 45, 32, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 1, 1, 45, 45, 45, 45, 32, 6, 1, 1, 4, 4, 3, 4, 1, 45, 45] 45 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 35, 36]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003690 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CC=N3)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 32, 32, 44, 44, 44, 44, 45, 45, 44, 45, 45, 44, 44, 1, 1, 1, 1, 9, 32, 44, 44, 45, 45, 44, 45, 44, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003690 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003690 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003690/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003690 Building REAL300000003691 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003691' /scratch/stefan/7769584/working/building/REAL300000003691 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003691 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003691/0 /scratch/stefan/7769584/working/building/REAL300000003691 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/785 `/scratch/stefan/7769584/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=C(C)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003691 none CCCN1N=C(C)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 147, 94, 94, 94, 94, 94, 94, 94, 36, 36, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 149, 149, 149, 149, 149, 147, 147, 94, 94, 94, 36, 7, 1, 1, 1, 1] 149 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003691 none CCCN1N=C(C)C(Cl)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 61, 94, 94, 66, 77, 94, 94, 94, 94, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 13, 61, 94, 94, 94, 94] 149 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 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: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003691 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003691 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003691/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003691 Building REAL300000003692 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003692' /scratch/stefan/7769584/working/building/REAL300000003692 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003692 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003692/0 /scratch/stefan/7769584/working/building/REAL300000003692 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/786 `/scratch/stefan/7769584/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2CC2)C=C1) `REAL300000003692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003692 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 18, 88, 85, 171, 201, 201, 198, 200, 201, 201, 201, 201, 20, 58, 58, 11, 1, 1, 1, 1, 58, 58, 91, 85, 85, 171, 201, 201, 201, 201, 58, 58, 1, 1, 1, 1, 1, 58, 58] 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: 659 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003692 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 42, 109, 109, 60, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 13, 58, 58, 1, 1, 7, 7, 7, 42, 109, 109, 109, 109, 1, 1, 58, 58, 58, 58, 58, 1, 1] 201 rigid atoms, others: [32, 1, 38, 39, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 516 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: REAL300000003692 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 109, 109, 66, 70, 185, 201, 201, 109, 109, 37, 37, 37, 7, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 109, 109] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 514 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003692 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003692 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003692/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003692 Building REAL300000003693 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003693' /scratch/stefan/7769584/working/building/REAL300000003693 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003693 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003693/0 /scratch/stefan/7769584/working/building/REAL300000003693 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/787 `/scratch/stefan/7769584/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(CC)CC(CC)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003693 none CCCCC(CC)CC(CC)N=NC1=CC=C(C(=O)[O-])C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 169, 148, 82, 52, 82, 124, 21, 4, 21, 29, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 192, 193, 193, 193, 193, 169, 169, 148, 148, 82, 124, 124, 124, 124, 124, 52, 52, 21, 34, 34, 34, 34, 34, 1, 1, 1, 1] 201 rigid atoms, others: [48, 46, 12, 45, 14, 15, 16, 17, 20, 21, 47, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1275 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003693 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003693 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003693/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003693 Building REAL300000003694 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003694' /scratch/stefan/7769584/working/building/REAL300000003694 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003694 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003694/0 /scratch/stefan/7769584/working/building/REAL300000003694 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/788 `/scratch/stefan/7769584/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC(Cl)=C1) `REAL300000003694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003694 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC(Cl)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 1, 9, 9, 42, 59, 59, 42, 50, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 42, 59, 59, 59, 59, 1, 1, 1] 63 rigid atoms, others: [32, 33, 2, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 285 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: REAL300000003694 none CCC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(Cl)=CC(Cl)=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [53, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 53, 53, 53, 36, 53, 53, 53, 54, 54, 54, 53, 53, 6, 1, 1, 1, 1, 53, 50, 53] 64 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 32, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 277 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003694 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003694 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003694/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003694 Building REAL300000003695 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003695' /scratch/stefan/7769584/working/building/REAL300000003695 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003695 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003695/0 /scratch/stefan/7769584/working/building/REAL300000003695 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/789 `/scratch/stefan/7769584/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CCC(F)(F)CC1) `REAL300000003695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003695 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 1, 5, 21, 21, 24, 24, 21, 21, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 5, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 2, 35, 36, 37, 38, 39, 40, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003695 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 21, 24, 24, 24, 24, 24, 23, 19, 19, 19, 19, 19, 15, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003695 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003695 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003695/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003695 Building REAL300000003696 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003696' /scratch/stefan/7769584/working/building/REAL300000003696 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003696 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003696/0 /scratch/stefan/7769584/working/building/REAL300000003696 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/790 `/scratch/stefan/7769584/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@@H+]3CC2=CC=CC=C2)C=C1) `REAL300000003696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003696 none O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@@H+]3CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 18, 19, 19, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [45, 46, 47, 48, 49, 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, 42, 43, 44, 50, 51]) total number of confs: 45 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003696 none O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@@H+]3CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [10, 9, 10, 8, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 5, 6, 6, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 10, 10] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 44 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: REAL300000003696 none O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@@H+]3CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 50, 51, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003696 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003696/1 /scratch/stefan/7769584/working/building/REAL300000003696 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/791 `/scratch/stefan/7769584/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@H+]3CC2=CC=CC=C2)C=C1) `REAL300000003696.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003696 none O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@H+]3CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 12, 13, 13, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 13, 13] 13 rigid atoms, others: [45, 46, 47, 48, 49, 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, 42, 43, 44, 50, 51]) total number of confs: 31 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003696 none O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@H+]3CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7] 13 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 26 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: REAL300000003696 none O=C([O-])C1=CC=C(N=NC2CCC3CCC(C2)[N@H+]3CC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', '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.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: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 50, 51, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003696 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003696 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003696/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003696/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003696 Building REAL300000003697 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003697' /scratch/stefan/7769584/working/building/REAL300000003697 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003697 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003697/0 /scratch/stefan/7769584/working/building/REAL300000003697 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/792 `/scratch/stefan/7769584/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(S(N)(=O)=O)=C1) `REAL300000003697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003697 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(S(N)(=O)=O)=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 1, 11, 11, 1, 1, 14, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 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: [78, 78, 37, 37, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 78, 78, 78, 158, 158, 158, 78, 78, 78, 78, 37, 7, 1, 1, 1, 1, 158, 158, 78] 158 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 495 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003697 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)SC(S(N)(=O)=O)=C1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 1, 11, 11, 1, 1, 14, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 57, 78, 78, 57, 74, 78, 78, 78, 78, 1, 1, 1, 5, 5, 5, 1, 2, 2, 2, 11, 57, 78, 78, 78, 78, 5, 5, 1] 158 rigid atoms, others: [0, 1, 2, 3, 33, 15, 16, 17, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003697 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003697 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003697/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003697 Building REAL300000003698 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003698' /scratch/stefan/7769584/working/building/REAL300000003698 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003698 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003698/0 /scratch/stefan/7769584/working/building/REAL300000003698 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/793 `/scratch/stefan/7769584/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(OC)CC2(CC(CN=NC3=CC=C(C(=O)[O-])C=C3)C2)C1) `REAL300000003698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003698 none COC1(OC)CC2(CC(CN=NC3=CC=C(C(=O)[O-])C=C3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 54, 54, 54, 63, 54, 54, 54, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 63, 63, 63, 63, 63, 63, 54, 54, 54, 54, 54, 22, 22, 1, 1, 1, 1, 54, 54, 54, 54] 63 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) 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: REAL300000003698 none COC1(OC)CC2(CC(CN=NC3=CC=C(C(=O)[O-])C=C3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 6, 1, 1, 1, 1, 1, 10, 45, 45, 54, 54, 45, 46, 54, 54, 54, 54, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 54, 54, 54, 54, 1, 1, 1, 1] 63 rigid atoms, others: [32, 1, 2, 3, 5, 6, 7, 8, 9, 42, 43, 40, 21, 22, 41, 33, 29, 30, 31] set([0, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003698 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003698 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003698/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003698 Building REAL300000003699 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003699' /scratch/stefan/7769584/working/building/REAL300000003699 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003699 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003699/0 /scratch/stefan/7769584/working/building/REAL300000003699 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/794 `/scratch/stefan/7769584/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=CC=C1) `REAL300000003699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003699 none COC1=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 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, 34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 34, 6, 1, 1, 1, 1, 52, 52, 52, 52] 52 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003699 none COC1=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 34, 52, 52, 35, 45, 52, 52, 52, 52, 1, 1, 1, 1, 1, 3, 3, 3, 1, 7, 34, 52, 52, 52, 52, 1, 1, 1, 1] 52 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 18, 19, 20, 21, 22, 36, 26, 35] set([0, 32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003699 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003699 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003699/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003699 Building REAL300000003700 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003700' /scratch/stefan/7769584/working/building/REAL300000003700 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003700 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003700/0 /scratch/stefan/7769584/working/building/REAL300000003700 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/795 `/scratch/stefan/7769584/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003700 none CC(C)N1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 18, 1, 1, 1, 1] 38 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003700 none CC(C)N1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 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, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 8, 38, 38, 38, 38] 38 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 33] set([0, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003700 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003700 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003700/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003700 Building REAL300000003701 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003701' /scratch/stefan/7769584/working/building/REAL300000003701 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003701 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003701/0 /scratch/stefan/7769584/working/building/REAL300000003701 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/796 `/scratch/stefan/7769584/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC(F)F)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003701 none CC1=CC=C(OC(F)F)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 60, 60, 60, 60, 60, 74, 78, 78, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 78, 24, 24, 1, 1, 1, 1] 78 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]) 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: REAL300000003701 none CC1=CC=C(OC(F)F)C(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 40, 40, 1, 1, 6, 38, 38, 60, 60, 38, 38, 60, 60, 60, 60, 1, 2, 2, 2, 1, 1, 40, 6, 6, 60, 60, 60, 60] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 22, 26, 27] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003701 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003701/1 /scratch/stefan/7769584/working/building/REAL300000003701 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/797 `/scratch/stefan/7769584/working/3D/797' -> `1.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(C(=O)[O-])C=C2)=N1) `REAL300000003701.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003701 none CC1=CC=C(OC(F)F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 2, 2, 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: [42, 42, 42, 42, 42, 42, 45, 51, 51, 24, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 51, 23, 6, 1, 1, 1, 1] 51 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]) 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: REAL300000003701 none CC1=CC=C(OC(F)F)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 2, 2, 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: [1, 1, 1, 1, 1, 1, 5, 21, 21, 1, 1, 6, 6, 26, 42, 42, 26, 26, 42, 42, 42, 42, 1, 2, 2, 2, 1, 1, 21, 6, 26, 42, 42, 42, 42] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 22, 26, 27] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003701 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003701 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003701/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003701/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003701 Building REAL300000003702 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003702' /scratch/stefan/7769584/working/building/REAL300000003702 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003702 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003702/0 /scratch/stefan/7769584/working/building/REAL300000003702 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/798 `/scratch/stefan/7769584/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2=CC=CO2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003702 none CN1N=C(C2=CC=CO2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 48, 66, 66, 66, 66, 48, 29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 48, 48, 48, 66, 66, 66, 48, 29, 7, 1, 1, 1, 1] 66 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 111 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003702 none CN1N=C(C2=CC=CO2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 11, 27, 27, 54, 66, 66, 66, 66, 66, 66, 66, 66, 11, 11, 11, 1, 1, 1, 11, 27, 54, 66, 66, 66, 66] 66 rigid atoms, others: [3, 4, 5, 6, 7, 8, 26, 27, 28] set([0, 1, 2, 9, 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: 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: REAL300000003702 none CN1N=C(C2=CC=CO2)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 1, 8, 8, 35, 48, 48, 44, 48, 48, 48, 48, 48, 2, 2, 2, 11, 11, 11, 1, 8, 35, 48, 48, 48, 48] 66 rigid atoms, others: [0, 1, 2, 3, 4, 9, 10, 11, 29] set([5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003702 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003702 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003702/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003702 Building REAL300000003703 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003703' /scratch/stefan/7769584/working/building/REAL300000003703 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003703 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003703/0 /scratch/stefan/7769584/working/building/REAL300000003703 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/799 `/scratch/stefan/7769584/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1) `REAL300000003703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003703 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [25, 3, 25, 104, 104, 109, 109, 104, 104, 109, 109, 109, 109, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 25, 25, 25, 25, 109, 109, 109, 109, 3, 1, 1, 1, 1, 1, 3, 3] 109 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003703 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 85, 85, 109, 109, 85, 85, 109, 109, 109, 109, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 13, 13, 13, 13, 109, 109, 109, 109, 1, 3, 3, 3, 3, 3, 1, 1] 109 rigid atoms, others: [1, 33, 40, 39, 13, 14, 15, 16, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003703 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [28, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 28, 28, 28, 28, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 109, 109] 109 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003703 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003703/1 /scratch/stefan/7769584/working/building/REAL300000003703 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/800 `/scratch/stefan/7769584/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1) `REAL300000003703.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003703 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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] 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, 3, 13, 13, 44, 49, 49, 46, 49, 49, 49, 49, 49, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 44, 49, 49, 49, 49, 3, 1, 1, 1, 1, 1, 3, 3] 49 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40]) total number of confs: 139 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003703 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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] 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: [7, 1, 7, 7, 30, 48, 48, 32, 35, 48, 48, 48, 48, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 8, 8, 8, 30, 48, 49, 48, 48, 1, 3, 3, 3, 3, 3, 1, 1] 49 rigid atoms, others: [1, 33, 40, 39, 13, 14, 15, 16, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003703 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C2=CC=CC=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'N.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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 28, 28, 28, 5, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49] 49 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 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: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003703 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003703 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003703/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003703/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003703 Building REAL300000003704 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003704' /scratch/stefan/7769584/working/building/REAL300000003704 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003704 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003704/0 /scratch/stefan/7769584/working/building/REAL300000003704 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/801 `/scratch/stefan/7769584/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3=CC=CC=C3)C=C2)C=C1) `REAL300000003704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003704 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 122, 145, 121, 145, 145, 121, 47, 47, 7, 4, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 18, 18, 145, 145, 145, 145, 121, 47, 18, 18, 4, 4, 1, 1, 1, 1, 1, 18, 18, 145, 145] 145 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38, 39, 40, 41]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003704 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [68, 37, 68, 36, 68, 68, 36, 7, 7, 1, 1, 1, 1, 1, 1, 8, 18, 19, 10, 19, 18, 1, 1, 68, 68, 68, 68, 36, 7, 1, 1, 8, 8, 18, 19, 11, 19, 18, 1, 1, 68, 68] 145 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 40, 41]) 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: REAL300000003704 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CC3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 39, 39, 68, 68, 39, 40, 136, 141, 141, 136, 141, 141, 68, 68, 1, 1, 1, 1, 9, 39, 68, 68, 136, 136, 141, 141, 136, 141, 141, 68, 68, 1, 1] 141 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003704 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003704 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003704/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003704 Building REAL300000003705 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003705' /scratch/stefan/7769584/working/building/REAL300000003705 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003705 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003705/0 /scratch/stefan/7769584/working/building/REAL300000003705 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/802 `/scratch/stefan/7769584/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Cl)=C2Br)C=C1) `REAL300000003705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003705 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Cl)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 16, 1, 1, 16, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 30, 8, 1, 1, 31, 31] 31 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003705 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CC(Cl)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 16, 1, 1, 16, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 25, 25, 31, 31, 31, 25, 31, 31, 31, 31, 1, 1, 1, 1, 10, 25, 31, 28, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003705 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003705 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003705/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003705 Building REAL300000003706 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003706' /scratch/stefan/7769584/working/building/REAL300000003706 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003706 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003706/0 /scratch/stefan/7769584/working/building/REAL300000003706 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/803 `/scratch/stefan/7769584/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000003706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003706 none CCCCC(=O)NC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=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', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 183, 83, 83, 83, 33, 22, 49, 49, 22, 22, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 49, 49, 197, 201, 201, 201, 201, 201, 201, 183, 183, 83, 49, 49, 22, 6, 1, 1, 1, 1, 49, 49] 201 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 839 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003706 none CCCCC(=O)NC1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=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', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 28, 49, 49, 28, 49, 49, 49, 49, 49, 1, 1, 58, 62, 62, 59, 59, 43, 43, 24, 24, 5, 1, 1, 6, 28, 49, 49, 49, 49, 1, 1] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 44, 43, 23, 24] set([0, 1, 2, 3, 4, 5, 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, 42]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003706 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003706 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003706/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003706 Building REAL300000003707 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003707' /scratch/stefan/7769584/working/building/REAL300000003707 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003707 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003707/0 /scratch/stefan/7769584/working/building/REAL300000003707 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/804 `/scratch/stefan/7769584/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC3(CC(COCC4=CC=CC=C4)C3)C2)C=C1) `REAL300000003707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003707 none O=C([O-])C1=CC=C(N=NC2CC3(CC(COCC4=CC=CC=C4)C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 46, 14, 3, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 118, 118, 118, 118, 118, 118, 46, 46, 3, 3, 1, 1, 1, 1, 1, 118, 118, 118, 118, 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: 519 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003707 none O=C([O-])C1=CC=C(N=NC2CC3(CC(COCC4=CC=CC=C4)C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 11, 15, 11, 16, 16, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 28, 65, 118, 118, 77, 118, 118, 1, 1, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 8, 8, 65, 65, 118, 118, 118, 118, 118, 1, 1, 1, 1, 16, 16] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 44, 46, 23, 24, 45, 47, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003707 none O=C([O-])C1=CC=C(N=NC2CC3(CC(COCC4=CC=CC=C4)C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 22, 22, 22, 22, 22, 74, 134, 201, 201, 201, 201, 201, 201, 22, 22, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 74, 74, 201, 201, 201, 201, 201, 201, 201, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 48, 49, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 694 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003707 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003707 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003707/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003707 Building REAL300000003708 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003708' /scratch/stefan/7769584/working/building/REAL300000003708 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003708 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003708/0 /scratch/stefan/7769584/working/building/REAL300000003708 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/805 `/scratch/stefan/7769584/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br) `REAL300000003708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003708 none COC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 73, 96, 73, 73, 73, 73, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 96, 96, 96, 73, 73, 73, 32, 6, 1, 1, 1, 1] 96 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003708 none COC(=O)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1Br 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 11, 11, 1, 1, 1, 17, 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, 2, 2, 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: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 57, 73, 73, 57, 57, 73, 73, 73, 73, 1, 1, 7, 7, 7, 1, 1, 1, 10, 57, 73, 73, 73, 73] 96 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 22, 26, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003708 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003708 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003708/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003708 Building REAL300000003709 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003709' /scratch/stefan/7769584/working/building/REAL300000003709 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003709 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003709/0 /scratch/stefan/7769584/working/building/REAL300000003709 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/806 `/scratch/stefan/7769584/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(OC(F)(F)F)C=C3)C2)C=C1) `REAL300000003709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003709 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(OC(F)(F)F)C=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [90, 74, 90, 71, 90, 90, 52, 52, 7, 7, 7, 1, 1, 1, 1, 1, 1, 12, 30, 29, 30, 1, 1, 7, 90, 90, 90, 90, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 90, 90] 135 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 329 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003709 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(OC(F)(F)F)C=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [42, 24, 41, 19, 42, 42, 13, 13, 1, 1, 1, 1, 1, 7, 7, 1, 1, 42, 65, 72, 71, 7, 7, 1, 42, 42, 42, 42, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 42, 42] 135 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 32, 33, 34, 35, 38, 39]) total number of confs: 354 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: REAL300000003709 none O=C([O-])C1=CC=C(N=NC2CC(C3=CC=C(OC(F)(F)F)C=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 5, 5, 43, 43, 43, 88, 88, 43, 67, 130, 130, 130, 130, 88, 88, 43, 1, 1, 1, 1, 43, 43, 43, 43, 88, 88, 88, 88, 43, 43, 1, 1] 130 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 39, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 401 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003709 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003709 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003709/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003709 Building REAL300000003710 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003710' /scratch/stefan/7769584/working/building/REAL300000003710 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003710 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003710/0 /scratch/stefan/7769584/working/building/REAL300000003710 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/807 `/scratch/stefan/7769584/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC=N1) `REAL300000003710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003710 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [13, 1, 13, 59, 59, 65, 65, 59, 59, 65, 65, 65, 65, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 13, 13, 13, 13, 65, 65, 65, 65, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 102 rigid atoms, others: [1, 41, 42, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003710 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 65, 65, 65, 102, 102, 102, 65, 65, 65, 23, 23, 23, 23, 1, 1, 1, 1, 65, 102, 102, 102, 102, 102, 102, 102, 102, 102, 65, 65] 102 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003710 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003710/1 /scratch/stefan/7769584/working/building/REAL300000003710 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/808 `/scratch/stefan/7769584/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC=N1) `REAL300000003710.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003710 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 23, 23, 19, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 8, 13, 23, 23, 23, 23, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 47 rigid atoms, others: [1, 41, 42, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003710 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 24, 24, 24, 47, 47, 47, 24, 24, 24, 22, 22, 22, 5, 1, 1, 1, 1, 24, 47, 47, 47, 47, 47, 47, 47, 47, 47, 24, 24] 47 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003710 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003710 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003710/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003710/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003710 Building REAL300000003711 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003711' /scratch/stefan/7769584/working/building/REAL300000003711 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003711 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003711/0 /scratch/stefan/7769584/working/building/REAL300000003711 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/809 `/scratch/stefan/7769584/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(OC)=C1C(C)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003711 none COC1=CC(Br)=CC(OC)=C1C(C)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 12, 5, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 18, 18, 1, 1, 1, 1] 21 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300000003711 none COC1=CC(Br)=CC(OC)=C1C(C)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 12, 5, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 4, 4, 15, 15, 21, 21, 15, 17, 21, 21, 21, 21, 3, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 27, 28] set([0, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003711 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003711/1 /scratch/stefan/7769584/working/building/REAL300000003711 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/810 `/scratch/stefan/7769584/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(OC)=C1C(C)=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003711.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003711 none COC1=CC(Br)=CC(OC)=C1C(C)=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 12, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 55, 55, 43, 55, 55, 55, 55, 57, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 57, 57, 57, 55, 55, 57, 57, 57, 27, 27, 27, 6, 1, 1, 1, 1] 57 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 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: REAL300000003711 none COC1=CC(Br)=CC(OC)=C1C(C)=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 12, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 9, 9, 9, 35, 55, 55, 35, 46, 55, 55, 55, 55, 3, 3, 3, 1, 1, 3, 3, 3, 10, 10, 10, 35, 55, 55, 55, 55] 57 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 27, 28] set([0, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 240 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003711 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003711 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003711/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003711/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003711 Building REAL300000003712 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003712' /scratch/stefan/7769584/working/building/REAL300000003712 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003712 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003712/0 /scratch/stefan/7769584/working/building/REAL300000003712 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/811 `/scratch/stefan/7769584/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C(OC)=C1) `REAL300000003712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003712 none COC1=CC(Br)=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 17, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 67, 51, 67, 67, 67, 33, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 79, 67, 79, 79, 79, 67, 33, 33, 33, 6, 1, 1, 1, 1, 79, 79, 79, 67] 79 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 228 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: REAL300000003712 none COC1=CC(Br)=C(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 17, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 28, 67, 67, 51, 67, 67, 67, 67, 67, 1, 1, 3, 1, 2, 2, 2, 1, 5, 5, 5, 28, 67, 67, 67, 67, 4, 4, 4, 1] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003712 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003712/1 /scratch/stefan/7769584/working/building/REAL300000003712 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/812 `/scratch/stefan/7769584/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(OC)=C1) `REAL300000003712.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003712 none COC1=CC(Br)=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 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, 16, 24, 24, 24, 15, 4, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 1, 1, 1, 1, 24, 24, 24, 24] 24 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) 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: REAL300000003712 none COC1=CC(Br)=C(C(C)N=NC2=CC=C(C(=O)[O-])C=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 24, 24, 17, 18, 24, 24, 24, 24, 1, 1, 3, 1, 2, 2, 2, 1, 4, 4, 4, 4, 24, 24, 24, 24, 3, 3, 3, 1] 24 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 20, 21, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003712 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003712 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003712/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003712/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003712 Building REAL300000003713 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003713' /scratch/stefan/7769584/working/building/REAL300000003713 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003713 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003713/0 /scratch/stefan/7769584/working/building/REAL300000003713 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/813 `/scratch/stefan/7769584/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C3CCS(=O)(=O)C3=CN2)C=C1) `REAL300000003713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003713 none O=C([O-])C1=CC=C(NN=CC2=C3CCS(=O)(=O)C3=CN2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 31, 38, 31, 38, 38, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 38, 38, 38, 30, 6, 1, 1, 1, 1, 1, 1, 37, 37] 38 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 33]) 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: REAL300000003713 none O=C([O-])C1=CC=C(NN=CC2=C3CCS(=O)(=O)C3=CN2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 26, 26, 38, 38, 38, 38, 38, 38, 38, 38, 37, 1, 1, 1, 1, 11, 26, 38, 38, 38, 38, 37, 37, 1, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003713 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003713 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003713/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003713 Building REAL300000003714 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003714' /scratch/stefan/7769584/working/building/REAL300000003714 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003714 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003714/0 /scratch/stefan/7769584/working/building/REAL300000003714 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/814 `/scratch/stefan/7769584/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCC3(CC3)C3=CC(F)=CC(F)=C32)C=C1) `REAL300000003714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003714 none O=C([O-])C1=CC=C(NN=C2CCC3(CC3)C3=CC(F)=CC(F)=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 39, 38, 23, 24, 25, 26, 27]) total number of confs: 30 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: REAL300000003714 none O=C([O-])C1=CC=C(NN=C2CCC3(CC3)C3=CC(F)=CC(F)=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 34 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003714 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003714 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003714/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003714 Building REAL300000003715 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003715' /scratch/stefan/7769584/working/building/REAL300000003715 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003715 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003715/0 /scratch/stefan/7769584/working/building/REAL300000003715 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/815 `/scratch/stefan/7769584/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(Br)=C2Br)C=C1) `REAL300000003715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003715 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Br)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 32, 28, 32, 32, 28, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 28, 10, 1, 1, 1, 32, 32] 32 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000003715 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(Br)=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 27, 27, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 11, 27, 32, 32, 32, 1, 1] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003715 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003715 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003715/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003715 Building REAL300000003716 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003716' /scratch/stefan/7769584/working/building/REAL300000003716 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003716 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003716/0 /scratch/stefan/7769584/working/building/REAL300000003716 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/816 `/scratch/stefan/7769584/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@H](N2N=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000003716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003716 none COC(=O)[C@H]1C[C@H](N2N=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 89, 179, 89, 89, 89, 67, 89, 67, 67, 67, 67, 34, 34, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 89, 179, 179, 179, 89, 89, 67, 67, 34, 7, 1, 1, 1, 1, 89, 89] 179 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 469 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003716 none COC(=O)[C@H]1C[C@H](N2N=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 7, 19, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 42, 67, 67, 42, 42, 67, 67, 67, 67, 7, 19, 19, 19, 7, 7, 1, 1, 10, 42, 67, 67, 67, 67, 7, 7] 179 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000003716 none COC(=O)[C@H]1C[C@H](N2N=CC=C2C=NNC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 70, 89, 89, 70, 70, 89, 89, 89, 89, 1, 4, 4, 4, 1, 1, 7, 7, 32, 70, 89, 89, 89, 89, 1, 1] 179 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 40, 41, 26, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003716 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003716 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003716/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003716 Building REAL300000003717 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003717' /scratch/stefan/7769584/working/building/REAL300000003717 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003717 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003717/0 /scratch/stefan/7769584/working/building/REAL300000003717 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/817 `/scratch/stefan/7769584/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003717 none CCN(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 177, 41, 177, 41, 128, 128, 41, 40, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 196, 197, 196, 196, 196, 177, 177, 177, 128, 128, 40, 6, 1, 1, 1, 1, 128, 128, 128, 128] 201 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 779 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: REAL300000003717 none CCN(C)C1=CC=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C(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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 1, 1, 12, 12, 76, 128, 128, 76, 78, 128, 128, 128, 128, 1, 1, 1, 19, 19, 19, 19, 19, 5, 5, 5, 1, 1, 12, 76, 128, 128, 128, 128, 2, 2, 2, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 42, 20, 21, 22, 31] set([0, 1, 3, 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, 40, 41]) total number of confs: 594 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003717 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003717/1 /scratch/stefan/7769584/working/building/REAL300000003717 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/818 `/scratch/stefan/7769584/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C=[NH+]NC2=CC=C(C(=O)[O-])C=C2)C(C)=C1) `REAL300000003717.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003717 none CCN(C)C1=CC=C(C=[NH+]NC2=CC=C(C(=O)[O-])C=C2)C(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', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [185, 157, 28, 157, 28, 103, 103, 28, 27, 6, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 189, 186, 185, 184, 185, 157, 159, 161, 103, 103, 27, 6, 1, 1, 1, 1, 103, 103, 103, 103] 189 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 782 number of broken/clashed sets: 189 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003717 none CCN(C)C1=CC=C(C=[NH+]NC2=CC=C(C(=O)[O-])C=C2)C(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', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 5, 1, 5, 1, 1, 1, 1, 1, 10, 10, 10, 52, 103, 103, 52, 54, 103, 103, 103, 103, 1, 1, 1, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 10, 52, 103, 103, 103, 103, 2, 2, 2, 1] 189 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 43, 21, 22, 23] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 471 number of broken/clashed sets: 189 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003717 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003717 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003717/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003717/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003717 Building REAL300000003718 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003718' /scratch/stefan/7769584/working/building/REAL300000003718 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003718 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003718/0 /scratch/stefan/7769584/working/building/REAL300000003718 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/819 `/scratch/stefan/7769584/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@H](N2C=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)C1) `REAL300000003718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003718 none COC(=O)[C@H]1C[C@H](N2C=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 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] 0 hydrogens need rotated 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, 201, 118, 118, 118, 47, 118, 47, 47, 47, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 118, 201, 201, 201, 118, 118, 47, 47, 19, 19, 1, 1, 1, 1, 118, 118] 201 rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 591 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003718 none COC(=O)[C@H]1C[C@H](N2C=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 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] 0 hydrogens 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, 8, 20, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 6, 34, 34, 47, 47, 34, 34, 47, 47, 47, 47, 1, 8, 20, 20, 20, 8, 8, 1, 1, 6, 6, 47, 47, 47, 47, 8, 8] 201 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003718 none COC(=O)[C@H]1C[C@H](N2C=CC(CN=NC3=CC=C(C(=O)[O-])C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 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] 0 hydrogens 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, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 32, 112, 112, 118, 118, 112, 112, 118, 118, 118, 118, 8, 1, 4, 4, 4, 1, 1, 8, 8, 32, 32, 118, 118, 118, 118, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 40, 41, 26, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003718 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003718/1 /scratch/stefan/7769584/working/building/REAL300000003718 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/820 `/scratch/stefan/7769584/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=N2)C1) `REAL300000003718.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003718 none COC(=O)[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 201, 116, 116, 116, 59, 116, 59, 59, 59, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 116, 201, 201, 201, 116, 116, 59, 59, 35, 7, 1, 1, 1, 1, 116, 116] 201 rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003718 none COC(=O)[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 30, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 7, 38, 59, 59, 42, 56, 59, 59, 59, 59, 1, 11, 30, 30, 30, 11, 11, 1, 1, 7, 38, 59, 59, 59, 59, 11, 11] 201 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003718 none COC(=O)[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(C(=O)[O-])C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 36, 36, 106, 116, 116, 114, 116, 116, 116, 116, 116, 11, 1, 4, 4, 4, 1, 1, 11, 11, 36, 106, 116, 116, 116, 116, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 40, 41, 26, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003718 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003718 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003718/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003718/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003718 Building REAL300000003719 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003719' /scratch/stefan/7769584/working/building/REAL300000003719 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003719 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003719/0 /scratch/stefan/7769584/working/building/REAL300000003719 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/821 `/scratch/stefan/7769584/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CN=C2Br)C=C1) `REAL300000003719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003719 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CN=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 16, 1, 8, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 28, 24, 28, 28, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 24, 8, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003719 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=CN=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 16, 1, 8, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 20, 20, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 20, 28, 28, 1, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003719 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003719 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003719/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003719 Building REAL300000003720 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003720' /scratch/stefan/7769584/working/building/REAL300000003720 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003720 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003720/0 /scratch/stefan/7769584/working/building/REAL300000003720 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/822 `/scratch/stefan/7769584/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=CC=N2)C=C1) `REAL300000003720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003720 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 46, 46, 46, 46, 40, 12, 3, 1, 1, 1, 1, 1, 3, 3, 46, 46] 46 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003720 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 46, 46, 29, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 46, 46, 46, 46, 29, 7, 1, 3, 3, 1, 3, 3, 1, 1, 46, 46] 46 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 19, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37]) 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: REAL300000003720 none O=C([O-])C1=CC=C(NN=CC2=CC(C3=CC=CC=C3)=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 9, 30, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 46 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003720 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003720/1 /scratch/stefan/7769584/working/building/REAL300000003720 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/823 `/scratch/stefan/7769584/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=CC=N2)C=C1) `REAL300000003720.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003720 none O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 79, 82, 79, 82, 82, 79, 79, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 82, 82, 82, 82, 17, 17, 3, 1, 1, 1, 1, 1, 3, 3, 82, 82] 82 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003720 none O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 66, 82, 66, 82, 82, 66, 66, 9, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 82, 82, 82, 82, 9, 9, 1, 3, 3, 2, 3, 3, 1, 1, 82, 82] 82 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 19, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37]) 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: REAL300000003720 none O=C([O-])C1=CC=C(N=NCC2=CC(C3=CC=CC=C3)=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 20, 20, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003720 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003720 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003720/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003720/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003720 Building REAL300000003721 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003721' /scratch/stefan/7769584/working/building/REAL300000003721 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003721 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003721/0 /scratch/stefan/7769584/working/building/REAL300000003721 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/824 `/scratch/stefan/7769584/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2O)C=C1) `REAL300000003721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003721 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 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: [20, 16, 20, 16, 20, 20, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 16, 6, 1, 1, 2, 20, 20] 40 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28, 29]) 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: REAL300000003721 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 1 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, 9, 18, 18, 20, 20, 20, 19, 20, 20, 20, 20, 1, 1, 1, 1, 9, 18, 20, 20, 40, 1, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 83 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003721 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003721/1 /scratch/stefan/7769584/working/building/REAL300000003721 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/825 `/scratch/stefan/7769584/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2[O-])C=C1) `REAL300000003721.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003721 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 8, 11, 11, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 8, 4, 1, 1, 11, 11] 11 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003721 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003721 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003721 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003721/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003721/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003721 Building REAL300000003722 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003722' /scratch/stefan/7769584/working/building/REAL300000003722 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003722 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003722/0 /scratch/stefan/7769584/working/building/REAL300000003722 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/826 `/scratch/stefan/7769584/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C(Cl)C(Cl)=CS2)C=C1) `REAL300000003722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003722 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C(Cl)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'Cl', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 16, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 35, 35, 31, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 31, 13, 1, 35, 35] 35 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 24, 25]) 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: REAL300000003722 none O=C([O-])C1=CC=C(NN=CC2=C(Cl)C(Cl)=CS2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'Cl', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 16, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 23, 23, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 9, 23, 35, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003722 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003722 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003722/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003722 Building REAL300000003723 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003723' /scratch/stefan/7769584/working/building/REAL300000003723 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003723 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003723/0 /scratch/stefan/7769584/working/building/REAL300000003723 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/827 `/scratch/stefan/7769584/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(C(=O)OCC)CC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)C2)C1) `REAL300000003723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003723 none CCOC(=O)C1(C(=O)OCC)CC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 5, 7, 7, 5, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 47, 47, 20, 47, 20, 20, 57, 57, 63, 115, 20, 20, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 94, 94, 94, 94, 94, 115, 115, 115, 115, 115, 20, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 710 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003723 none CCOC(=O)C1(C(=O)OCC)CC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 5, 7, 7, 5, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 5, 1, 5, 1, 1, 7, 7, 12, 27, 1, 1, 1, 1, 1, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [3, 47, 5, 6, 39, 38, 41, 42, 11, 12, 13, 14, 15, 48, 40, 50, 49, 26, 27] set([0, 1, 2, 4, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003723 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003723 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003723/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003723 Building REAL300000003724 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003724' /scratch/stefan/7769584/working/building/REAL300000003724 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003724 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003724/0 /scratch/stefan/7769584/working/building/REAL300000003724 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/828 `/scratch/stefan/7769584/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003724 none CC(C)(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 35, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 35, 6, 1, 1, 1, 1] 58 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 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: REAL300000003724 none CC(C)(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 8, 40, 58, 58, 40, 40, 58, 58, 58, 58, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 8, 40, 58, 58, 58, 58] 58 rigid atoms, others: [1, 43, 4, 5, 6, 7, 11, 12, 13] set([0, 2, 3, 8, 9, 10, 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, 44, 45, 46, 47, 48, 49]) total number of confs: 245 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003724 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003724 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003724/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003724 Building REAL300000003725 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003725' /scratch/stefan/7769584/working/building/REAL300000003725 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003725 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003725/0 /scratch/stefan/7769584/working/building/REAL300000003725 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/829 `/scratch/stefan/7769584/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=C2CCCCC3=C(Br)C=CC=C32)C=C1) `REAL300000003725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003725 none O=C([O-])C1=CC=C(NN=C2CCCCC3=C(Br)C=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 6, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 9 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 38, 37]) total number of confs: 35 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: REAL300000003725 none O=C([O-])C1=CC=C(NN=C2CCCCC3=C(Br)C=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 18 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003725 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003725 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003725/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003725 Building REAL300000003726 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003726' /scratch/stefan/7769584/working/building/REAL300000003726 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003726 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003726/0 /scratch/stefan/7769584/working/building/REAL300000003726 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/830 `/scratch/stefan/7769584/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(OC)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003726 none COC1=CC(C)=CC(OC)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 90, 90, 90, 39, 60, 90, 90, 90, 106, 38, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 90, 90, 90, 90, 90, 106, 106, 106, 38, 6, 1, 1, 1, 1] 106 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 460 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003726 none COC1=CC(C)=CC(OC)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 10, 10, 69, 94, 94, 71, 82, 94, 94, 94, 94, 4, 4, 4, 1, 2, 2, 2, 1, 3, 3, 3, 10, 69, 94, 94, 94, 94] 106 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 26, 30] set([0, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003726 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003726/1 /scratch/stefan/7769584/working/building/REAL300000003726 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/831 `/scratch/stefan/7769584/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(OC)=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003726.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003726 none COC1=CC(C)=CC(OC)=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 40, 40, 40, 26, 26, 40, 40, 40, 46, 26, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 46, 46, 46, 40, 40, 40, 40, 40, 46, 46, 46, 26, 26, 1, 1, 1, 1] 46 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300000003726 none COC1=CC(C)=CC(OC)=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 5, 31, 31, 41, 41, 32, 32, 41, 41, 41, 41, 4, 4, 4, 1, 2, 2, 2, 1, 4, 4, 4, 5, 5, 41, 41, 41, 41] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 26, 30] set([0, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003726 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003726 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003726/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003726/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003726 Building REAL300000003727 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003727' /scratch/stefan/7769584/working/building/REAL300000003727 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003727 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003727/0 /scratch/stefan/7769584/working/building/REAL300000003727 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/832 `/scratch/stefan/7769584/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C)C(Br)=C1) `REAL300000003727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003727 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 17, 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, 2, 2, 7, 7, 7, 7, 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: [11, 1, 11, 11, 45, 55, 55, 51, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 45, 55, 55, 55, 55, 1, 1, 2, 2, 2, 1] 55 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 157 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003727 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 17, 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, 2, 2, 7, 7, 7, 7, 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: [29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 55, 55, 54, 55, 55, 55, 55, 30, 30, 30, 5, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003727 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003727 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003727/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003727 Building REAL300000003728 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003728' /scratch/stefan/7769584/working/building/REAL300000003728 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003728 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003728/0 /scratch/stefan/7769584/working/building/REAL300000003728 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/833 `/scratch/stefan/7769584/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1F) `REAL300000003728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003728 none COC1=CC=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1F NO_LONG_NAME dock atom types: ['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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 31, 31, 31, 7, 1, 1, 1, 1] 93 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 133 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: REAL300000003728 none COC1=CC=CC(C(C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1F NO_LONG_NAME dock atom types: ['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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 93, 93, 77, 93, 93, 93, 93, 93, 1, 1, 3, 4, 4, 1, 1, 1, 13, 13, 13, 63, 93, 93, 93, 93] 93 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003728 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003728 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003728/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003728 Building REAL300000003729 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003729' /scratch/stefan/7769584/working/building/REAL300000003729 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003729 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003729/0 /scratch/stefan/7769584/working/building/REAL300000003729 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/834 `/scratch/stefan/7769584/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CN=C3SC(Br)=CN23)C=C1) `REAL300000003729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003729 none O=C([O-])C1=CC=C(NN=CC2=CN=C3SC(Br)=CN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 14, 1, 17, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 41, 41, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 36, 9, 1, 1, 41, 41] 41 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003729 none O=C([O-])C1=CC=C(NN=CC2=CN=C3SC(Br)=CN23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 14, 1, 17, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 27, 27, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 11, 27, 41, 41, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003729 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003729 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003729/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003729 Building REAL300000003730 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003730' /scratch/stefan/7769584/working/building/REAL300000003730 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003730 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003730/0 /scratch/stefan/7769584/working/building/REAL300000003730 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/835 `/scratch/stefan/7769584/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(F)=CC=C2S1) `REAL300000003730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003730 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', '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, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 14, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 24, 24, 24, 24, 24, 24, 24, 14, 6, 1, 1, 1, 1, 24, 24] 24 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003730 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(C(=O)[O-])C=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', '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, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 13, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 9, 13, 24, 24, 24, 24, 1, 1] 24 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 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/7769584/working/building/REAL300000003730 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003730 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003730/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003730 Building REAL300000003731 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003731' /scratch/stefan/7769584/working/building/REAL300000003731 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003731 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003731/0 /scratch/stefan/7769584/working/building/REAL300000003731 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/836 `/scratch/stefan/7769584/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)(F)F)C(Cl)=C2)C=C1) `REAL300000003731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003731 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)(F)F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [96, 56, 96, 56, 96, 96, 56, 10, 10, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 1, 1, 1, 96, 96, 96, 96, 56, 10, 1, 1, 1, 96, 96] 143 rigid atoms, others: [9, 10, 11, 12, 13, 14, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003731 none O=C([O-])C1=CC=C(NN=CC2=CC=C(OC(F)(F)F)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 46, 46, 126, 126, 82, 126, 192, 192, 192, 192, 126, 126, 126, 1, 1, 1, 1, 11, 46, 126, 126, 126, 1, 1] 192 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003731 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003731 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003731/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003731 Building REAL300000003732 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003732' /scratch/stefan/7769584/working/building/REAL300000003732 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003732 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003732/0 /scratch/stefan/7769584/working/building/REAL300000003732 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/837 `/scratch/stefan/7769584/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CC(F)(F)C3(F)F)=C2)C=C1) `REAL300000003732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003732 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CC(F)(F)C3(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 164, 184, 164, 184, 184, 164, 46, 46, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 184, 184, 184, 184, 164, 46, 6, 6, 6, 1, 1, 1, 6, 184, 184] 184 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003732 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CC(F)(F)C3(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [107, 67, 107, 67, 107, 107, 67, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 107, 107, 107, 107, 67, 11, 1, 1, 1, 6, 6, 6, 1, 107, 107] 184 rigid atoms, others: [32, 36, 9, 10, 11, 12, 13, 14, 15, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003732 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C3CC(F)(F)C3(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 40, 40, 108, 108, 40, 108, 108, 181, 181, 181, 181, 181, 181, 181, 108, 1, 1, 1, 1, 11, 40, 108, 108, 69, 181, 181, 181, 108, 1, 1] 181 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003732 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003732 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003732/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003732 Building REAL300000003733 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003733' /scratch/stefan/7769584/working/building/REAL300000003733 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003733 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003733/0 /scratch/stefan/7769584/working/building/REAL300000003733 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/838 `/scratch/stefan/7769584/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=NC=C3)C=C2)C=C1) `REAL300000003733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003733 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=NC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 19, 8, 8, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 25, 25, 25, 19, 8, 3, 3, 1, 1, 1, 1, 3, 3, 25, 25] 25 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, 36, 37]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003733 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=NC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 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, 21, 25, 25, 16, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 25, 25, 25, 25, 16, 5, 1, 1, 3, 3, 3, 3, 1, 1, 25, 25] 25 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36, 37]) 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: REAL300000003733 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=NC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 23, 23, 25, 25, 23, 23, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 23, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003733 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003733 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003733/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003733 Building REAL300000003734 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003734' /scratch/stefan/7769584/working/building/REAL300000003734 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003734 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003734/0 /scratch/stefan/7769584/working/building/REAL300000003734 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/839 `/scratch/stefan/7769584/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[Si](C)(C)OC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003734 none CC(C)(C)[Si](C)(C)OC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'Si', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 24, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 149, 201, 201, 101, 101, 101, 101, 101, 32, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 31, 6, 1, 1, 1, 1, 101] 201 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50]) total number of confs: 519 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003734 none CC(C)(C)[Si](C)(C)OC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'Si', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 24, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 60, 101, 101, 64, 69, 101, 101, 101, 101, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 1, 1, 1, 13, 60, 101, 101, 101, 101, 1] 201 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49]) total number of confs: 462 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003734 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003734 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003734/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003734 Building REAL300000003735 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003735' /scratch/stefan/7769584/working/building/REAL300000003735 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003735 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003735/0 /scratch/stefan/7769584/working/building/REAL300000003735 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/840 `/scratch/stefan/7769584/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=C1) `REAL300000003735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003735 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 92, 176, 92, 92, 29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 92, 92, 92, 92, 92, 92, 92, 176, 176, 176, 92, 29, 7, 1, 1, 1, 1, 92, 92] 176 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) 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: REAL300000003735 none COC(=O)C1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 12, 12, 64, 92, 92, 87, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 1, 12, 64, 92, 92, 92, 92, 1, 1] 176 rigid atoms, others: [2, 4, 5, 6, 7, 37, 19, 20, 21, 22, 23, 24, 25, 29, 36] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003735 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003735 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003735/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003735 Building REAL300000003736 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003736' /scratch/stefan/7769584/working/building/REAL300000003736 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003736 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003736/0 /scratch/stefan/7769584/working/building/REAL300000003736 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/841 `/scratch/stefan/7769584/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)N2)C=C1) `REAL300000003736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003736 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 86, 94, 94, 86, 38, 37, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 93, 94, 94, 94, 86, 38, 13, 13, 1, 1, 1, 13, 94, 94] 94 rigid atoms, others: [13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 287 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003736 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [49, 39, 49, 37, 49, 49, 37, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 49, 49, 49, 49, 37, 7, 1, 1, 13, 13, 13, 1, 49, 49] 94 rigid atoms, others: [9, 10, 11, 12, 13, 14, 19, 26, 27, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33]) 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: REAL300000003736 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C3=CC=CS3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 33, 34, 49, 49, 49, 49, 82, 82, 82, 82, 49, 1, 1, 1, 1, 12, 33, 49, 49, 82, 82, 82, 49, 1, 1] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003736 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003736 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003736/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003736 Building REAL300000003737 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003737' /scratch/stefan/7769584/working/building/REAL300000003737 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003737 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003737/0 /scratch/stefan/7769584/working/building/REAL300000003737 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/842 `/scratch/stefan/7769584/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC=C1C(F)(F)F) `REAL300000003737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003737 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC=C1C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 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, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 16, 25, 25, 16, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 16, 25, 25, 25, 25, 1, 1, 1] 25 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 94 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003737 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CN=CC=C1C(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 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, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 18, 18, 18, 5, 1, 1, 1, 1, 25, 25, 25] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003737 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003737 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003737/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003737 Building REAL300000003738 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003738' /scratch/stefan/7769584/working/building/REAL300000003738 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003738 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003738/0 /scratch/stefan/7769584/working/building/REAL300000003738 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/843 `/scratch/stefan/7769584/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)C(Cl)=C1) `REAL300000003738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003738 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)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', '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', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 41, 57, 57, 55, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 57, 57, 57, 57, 1, 1, 1] 57 rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003738 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)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', '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', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 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, 2, 2, 7, 7, 7, 7, 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: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 27, 27, 27, 6, 1, 1, 1, 1, 57, 57, 57] 57 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003738 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003738 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003738/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003738 Building REAL300000003739 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003739' /scratch/stefan/7769584/working/building/REAL300000003739 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003739 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003739/0 /scratch/stefan/7769584/working/building/REAL300000003739 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/844 `/scratch/stefan/7769584/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)C2)C1) `REAL300000003739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003739 none COC(=O)C1CC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)C2)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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 6, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 16 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003739 none COC(=O)C1CC2(CC(N=NC3=CC=C(C(=O)[O-])C=C3)C2)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', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1] 16 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 38, 37, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([0, 1, 34, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003739 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003739 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003739/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003739 Building REAL300000003740 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003740' /scratch/stefan/7769584/working/building/REAL300000003740 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003740 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003740/0 /scratch/stefan/7769584/working/building/REAL300000003740 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/845 `/scratch/stefan/7769584/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=C1) `REAL300000003740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003740 none COC1=CC(C)=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 47, 33, 6, 1, 1, 1, 1, 49, 49] 49 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003740 none COC1=CC(C)=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 36, 49, 49, 36, 44, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2, 1, 7, 36, 49, 49, 49, 49, 1, 1] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 21, 22, 23, 27, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003740 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003740 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003740/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003740 Building REAL300000003741 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003741' /scratch/stefan/7769584/working/building/REAL300000003741 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003741 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003741/0 /scratch/stefan/7769584/working/building/REAL300000003741 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/846 `/scratch/stefan/7769584/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C(F)(F)F) `REAL300000003741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003741 none CC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C(F)(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 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, 2, 2, 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, 21, 21, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 6, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003741 none CC1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1C(F)(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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 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, 2, 2, 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, 10, 10, 27, 31, 31, 27, 31, 31, 31, 31, 31, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 10, 27, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003741 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003741 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003741/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003741 Building REAL300000003742 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003742' /scratch/stefan/7769584/working/building/REAL300000003742 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003742 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003742/0 /scratch/stefan/7769584/working/building/REAL300000003742 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/847 `/scratch/stefan/7769584/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2Br)C=C1) `REAL300000003742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003742 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 28, 24, 28, 28, 24, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 28, 28, 28, 28, 24, 8, 1, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003742 none O=C([O-])C1=CC=C(NN=CC2=CC=C(C(F)(F)F)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 28, 28, 24, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 20, 28, 28, 28, 1, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003742 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003742 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003742/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003742 Building REAL300000003743 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003743' /scratch/stefan/7769584/working/building/REAL300000003743 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003743 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003743/0 /scratch/stefan/7769584/working/building/REAL300000003743 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/848 `/scratch/stefan/7769584/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=NC=C(Br)C=C3O2)C=C1) `REAL300000003743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003743 none O=C([O-])C1=CC=C(NN=CC2=CC3=NC=C(Br)C=C3O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 27, 28, 28, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 28, 28, 28, 19, 6, 1, 1, 1, 27, 27] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000003743 none O=C([O-])C1=CC=C(NN=CC2=CC3=NC=C(Br)C=C3O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 20, 21, 27, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 11, 20, 27, 28, 28, 1, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003743 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003743 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003743/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003743 Building REAL300000003744 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003744' /scratch/stefan/7769584/working/building/REAL300000003744 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003744 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003744/0 /scratch/stefan/7769584/working/building/REAL300000003744 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/849 `/scratch/stefan/7769584/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC2=C1CCC2(C)C) `REAL300000003744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003744 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC2=C1CCC2(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 61, 156, 156, 61, 61, 156, 156, 156, 156, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 61, 156, 156, 156, 156, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 156 rigid atoms, others: [1, 27, 36, 48, 46, 13, 14, 15, 16, 49, 50, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56]) total number of confs: 753 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: REAL300000003744 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(C)(C)C)=CC2=C1CCC2(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 37, 37, 37, 6, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156] 156 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 208 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003744 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003744 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003744/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003744 Building REAL300000003745 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003745' /scratch/stefan/7769584/working/building/REAL300000003745 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003745 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003745/0 /scratch/stefan/7769584/working/building/REAL300000003745 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/850 `/scratch/stefan/7769584/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(C(CC(C)C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003745 none CC1=CC(Br)=CC(C(CC(C)C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [90, 90, 69, 89, 89, 89, 27, 27, 27, 47, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 75, 89, 47, 47, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 90] 97 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 320 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: REAL300000003745 none CC1=CC(Br)=CC(C(CC(C)C)=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 35, 38, 38, 12, 12, 67, 89, 89, 67, 68, 89, 90, 90, 90, 1, 2, 2, 2, 1, 1, 35, 35, 38, 38, 38, 38, 38, 38, 38, 67, 89, 89, 90, 90, 1] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 23, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 476 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003745 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003745 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003745/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003745 Building REAL300000003746 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003746' /scratch/stefan/7769584/working/building/REAL300000003746 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003746 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003746/0 /scratch/stefan/7769584/working/building/REAL300000003746 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/851 `/scratch/stefan/7769584/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=C3SC(C(F)F)=NC3=CC=C2)C=C1) `REAL300000003746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003746 none O=C([O-])C1=CC=C(NN=CC2=C3SC(C(F)F)=NC3=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [69, 62, 69, 55, 69, 69, 52, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 1, 1, 69, 69, 69, 69, 52, 12, 12, 1, 1, 1, 69, 69] 104 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 33, 32, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000003746 none O=C([O-])C1=CC=C(NN=CC2=C3SC(C(F)F)=NC3=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 8, 15, 15, 40, 40, 40, 40, 60, 60, 40, 40, 40, 40, 40, 1, 1, 1, 1, 8, 15, 60, 40, 40, 40, 1, 1] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 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/7769584/working/building/REAL300000003746 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003746 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003746/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003746 Building REAL300000003747 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003747' /scratch/stefan/7769584/working/building/REAL300000003747 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003747 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003747/0 /scratch/stefan/7769584/working/building/REAL300000003747 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/852 `/scratch/stefan/7769584/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003747 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 19, 5, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 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: REAL300000003747 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 30, 30, 26, 26, 30, 30, 30, 30, 3, 3, 3, 1, 1, 1, 6, 26, 30, 30, 30, 30] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003747 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003747 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003747/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003747 Building REAL300000003748 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003748' /scratch/stefan/7769584/working/building/REAL300000003748 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003748 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003748/0 /scratch/stefan/7769584/working/building/REAL300000003748 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/853 `/scratch/stefan/7769584/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003748 none CC(F)(F)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 72, 107, 107, 72, 72, 72, 72, 35, 35, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 72, 107, 107, 107, 72, 72, 72, 35, 6, 1, 1, 1, 1] 107 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000003748 none CC(F)(F)C1=CC=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 4, 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 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, 1, 1, 1, 1, 1, 1, 9, 9, 48, 72, 72, 48, 48, 72, 72, 72, 72, 1, 10, 10, 10, 1, 1, 1, 9, 48, 72, 72, 72, 72] 107 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003748 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003748/1 /scratch/stefan/7769584/working/building/REAL300000003748 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/854 `/scratch/stefan/7769584/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1) `REAL300000003748.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003748 none CC(F)(F)C1=CC=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 99, 182, 182, 99, 99, 99, 99, 24, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 99, 182, 182, 182, 99, 99, 99, 24, 24, 1, 1, 1, 1] 182 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 642 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003748 none CC(F)(F)C1=CC=CC(CN=NC2=CC=C(C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 9, 76, 76, 99, 99, 81, 99, 99, 99, 99, 99, 1, 12, 12, 12, 1, 1, 1, 9, 9, 99, 99, 99, 99] 182 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003748 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003748 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003748/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003748/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003748 Building REAL300000003749 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003749' /scratch/stefan/7769584/working/building/REAL300000003749 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003749 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003749/0 /scratch/stefan/7769584/working/building/REAL300000003749 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/855 `/scratch/stefan/7769584/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(CCOC3)N=C2Cl)C=C1) `REAL300000003749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003749 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(CCOC3)N=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 12, 5, 8, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 18, 21, 18, 21, 21, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 18, 7, 1, 1, 1, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 21, 22, 23, 24, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003749 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(CCOC3)N=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 12, 5, 8, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 8, 17, 21, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003749 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003749 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003749/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003749 Building REAL300000003750 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003750' /scratch/stefan/7769584/working/building/REAL300000003750 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003750 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003750/0 /scratch/stefan/7769584/working/building/REAL300000003750 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/856 `/scratch/stefan/7769584/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=C1) `REAL300000003750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003750 none COC1=CC(OC)=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [87, 71, 71, 71, 71, 71, 88, 71, 71, 41, 41, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 88, 88, 88, 71, 88, 88, 88, 71, 41, 6, 1, 1, 1, 1, 71, 71] 88 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) 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: REAL300000003750 none COC1=CC(OC)=C2C=C(C=NNC3=CC=C(C(=O)[O-])C=C3)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 7, 7, 43, 71, 71, 43, 43, 71, 71, 71, 71, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 7, 43, 71, 71, 71, 71, 1, 1] 88 rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 39, 40, 22, 23, 24, 28] set([0, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003750 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003750 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003750/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003750 Building REAL300000003751 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003751' /scratch/stefan/7769584/working/building/REAL300000003751 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003751 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003751/0 /scratch/stefan/7769584/working/building/REAL300000003751 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/857 `/scratch/stefan/7769584/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1) `REAL300000003751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003751 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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: [52, 40, 52, 40, 52, 52, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 52, 52, 52, 52, 40, 10, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 17, 18, 19, 23, 24, 25, 26, 27, 28, 35]) 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: REAL300000003751 none O=C([O-])C1=CC=C(NN=CC2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 9, 33, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003751 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003751/1 /scratch/stefan/7769584/working/building/REAL300000003751 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/858 `/scratch/stefan/7769584/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1) `REAL300000003751.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003751 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 42, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 42, 42] 42 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 17, 18, 19, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003751 none O=C([O-])C1=CC=C(N=NCC2=CNC3=CC(C(F)(F)F)=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 16, 16, 42, 42, 42, 42, 42, 1, 1] 42 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003751 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003751 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003751/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003751/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003751 Building REAL300000003752 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003752' /scratch/stefan/7769584/working/building/REAL300000003752 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003752 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003752/0 /scratch/stefan/7769584/working/building/REAL300000003752 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/859 `/scratch/stefan/7769584/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC(Br)=CC=C3S2)C=C1) `REAL300000003752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003752 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC(Br)=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 34, 36, 36, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 36, 36, 36, 28, 8, 1, 1, 1, 1, 35, 35] 36 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003752 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC(Br)=CC=C3S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 10, 27, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003752 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003752 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003752/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003752 Building REAL300000003753 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003753' /scratch/stefan/7769584/working/building/REAL300000003753 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003753 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003753/0 /scratch/stefan/7769584/working/building/REAL300000003753 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/860 `/scratch/stefan/7769584/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Cl)=C1C) `REAL300000003753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003753 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 31, 41, 41, 33, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2] 41 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003753 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 41, 41, 41, 41, 41, 41, 41, 30, 30, 30, 6, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003753 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003753 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003753/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003753 Building REAL300000003754 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003754' /scratch/stefan/7769584/working/building/REAL300000003754 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003754 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003754/0 /scratch/stefan/7769584/working/building/REAL300000003754 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/861 `/scratch/stefan/7769584/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003754 none CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [60, 60, 60, 60, 187, 201, 201, 188, 201, 201, 60, 59, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 187, 187, 201, 201, 201, 201, 201, 60, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 731 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003754 none CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 14, 66, 66, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003754 none CN1C(CC2=CC=CC=C2)=CN=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 8, 14, 14, 9, 14, 14, 1, 1, 1, 1, 8, 48, 48, 59, 59, 48, 48, 59, 59, 59, 59, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 1, 8, 8, 59, 59, 60, 59] 201 rigid atoms, others: [0, 1, 2, 3, 10, 11, 12, 13, 35] set([4, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003754 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003754 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003754/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003754 Building REAL300000003755 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003755' /scratch/stefan/7769584/working/building/REAL300000003755 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003755 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003755/0 /scratch/stefan/7769584/working/building/REAL300000003755 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/862 `/scratch/stefan/7769584/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1) `REAL300000003755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003755 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [56, 11, 56, 56, 180, 201, 201, 186, 201, 201, 201, 201, 201, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 56, 56, 56, 180, 201, 201, 201, 201, 11, 11, 1, 1, 1, 8, 8, 24, 1] 603 rigid atoms, others: [36, 37, 38, 42, 16, 17, 18, 19, 20, 21, 22, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 621 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003755 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 71, 71, 40, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 11, 11, 1, 11, 11, 67, 11, 1, 8, 8, 8, 39, 71, 71, 71, 71, 1, 1, 11, 11, 1, 67, 67, 201, 11] 603 rigid atoms, others: [1, 34, 35, 13, 14, 15, 16, 17, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 692 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: REAL300000003755 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 71, 71, 71, 71, 201, 201, 123, 201, 201, 201, 201, 71, 20, 20, 20, 4, 1, 1, 1, 1, 71, 71, 201, 201, 177, 201, 201, 603, 201] 603 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 11, 12, 30, 31] set([0, 1, 2, 9, 10, 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: 1144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003755 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003755/1 /scratch/stefan/7769584/working/building/REAL300000003755 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/863 `/scratch/stefan/7769584/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1) `REAL300000003755.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003755 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [74, 12, 74, 186, 186, 196, 196, 186, 186, 196, 196, 196, 196, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 1, 12, 74, 74, 74, 74, 196, 196, 196, 196, 12, 12, 1, 1, 1, 6, 6, 18, 1] 603 rigid atoms, others: [36, 37, 38, 42, 16, 17, 18, 19, 20, 21, 22, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003755 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 45, 45, 56, 56, 45, 45, 56, 56, 56, 56, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 52, 12, 1, 11, 11, 11, 11, 56, 56, 56, 56, 1, 1, 12, 12, 1, 52, 52, 156, 12] 603 rigid atoms, others: [1, 34, 35, 13, 14, 15, 16, 17, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003755 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 56, 56, 56, 56, 196, 196, 56, 196, 196, 201, 196, 56, 15, 15, 15, 15, 1, 1, 1, 1, 56, 56, 196, 196, 60, 201, 201, 603, 196] 603 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 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: 1152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003755 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003755 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003755/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003755/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003755 Building REAL300000003756 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003756' /scratch/stefan/7769584/working/building/REAL300000003756 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003756 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003756/0 /scratch/stefan/7769584/working/building/REAL300000003756 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/864 `/scratch/stefan/7769584/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CC2=CC=CC=C2C1) `REAL300000003756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003756 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 1, 3, 15, 15, 21, 21, 15, 15, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 3, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [33, 2, 35, 36, 37, 38, 39, 40, 41, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 99 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003756 none CCC(N=NC1=CC=C(C(=O)[O-])C=C1)C1CC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 18, 18, 18, 16, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 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: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003756 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003756 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003756/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003756 Building REAL300000003757 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003757' /scratch/stefan/7769584/working/building/REAL300000003757 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003757 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003757/0 /scratch/stefan/7769584/working/building/REAL300000003757 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/865 `/scratch/stefan/7769584/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C(F)(F)F)=C1) `REAL300000003757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003757 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 54, 54, 54, 54, 2, 2, 2, 1] 54 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000003757 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=NN(C)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 54, 54, 54, 54, 54, 54, 54, 54, 54, 21, 21, 21, 21, 1, 1, 1, 1, 54, 54, 54, 54] 54 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003757 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003757 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003757/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003757 Building REAL300000003758 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003758' /scratch/stefan/7769584/working/building/REAL300000003758 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003758 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003758/0 /scratch/stefan/7769584/working/building/REAL300000003758 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/866 `/scratch/stefan/7769584/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CP(C)(=O)C1CCCC(N=NC2=CC=C(C(=O)[O-])C=C2)C1) `REAL300000003758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003758 none CP(C)(=O)C1CCCC(N=NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'P.3', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 13, 5, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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, 13, 22, 22, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 22, 22, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13] 22 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003758 none CP(C)(=O)C1CCCC(N=NC2=CC=C(C(=O)[O-])C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'P.3', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 13, 5, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 8, 13, 13, 13, 13, 13, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1] 22 rigid atoms, others: [32, 1, 34, 4, 5, 6, 7, 8, 9, 39, 40, 20, 33, 27, 28, 29, 30, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003758 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003758 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003758/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003758 Building REAL300000003759 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003759' /scratch/stefan/7769584/working/building/REAL300000003759 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003759 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003759/0 /scratch/stefan/7769584/working/building/REAL300000003759 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/867 `/scratch/stefan/7769584/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1) `REAL300000003759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003759 none O=C([O-])C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 199, 201, 197, 201, 201, 197, 197, 44, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 201, 201, 201, 201, 44, 44, 1, 1, 1, 1, 12, 12, 201, 201] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 369 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003759 none O=C([O-])C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 48, 74, 44, 74, 74, 44, 44, 8, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 12, 1, 1, 74, 74, 74, 74, 8, 8, 12, 12, 12, 12, 1, 1, 74, 74] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003759 none O=C([O-])C1=CC=C(N=NCC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 39, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 86, 86, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003759 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003759/1 /scratch/stefan/7769584/working/building/REAL300000003759 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/868 `/scratch/stefan/7769584/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1) `REAL300000003759.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003759 none O=C([O-])C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 45, 55, 42, 55, 55, 42, 12, 12, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 8, 8, 55, 55, 55, 55, 42, 12, 1, 1, 1, 1, 8, 8, 55, 55] 55 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003759 none O=C([O-])C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 25, 13, 25, 25, 13, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 8, 1, 1, 25, 25, 25, 25, 13, 4, 8, 8, 8, 8, 1, 1, 25, 25] 55 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) 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: REAL300000003759 none O=C([O-])C1=CC=C(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 39, 39, 53, 53, 53, 123, 123, 123, 123, 123, 123, 123, 123, 53, 53, 1, 1, 1, 1, 10, 39, 123, 123, 123, 123, 53, 53, 1, 1] 123 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003759 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003759 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003759/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003759/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003759 Building REAL300000003760 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003760' /scratch/stefan/7769584/working/building/REAL300000003760 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003760 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003760/0 /scratch/stefan/7769584/working/building/REAL300000003760 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/869 `/scratch/stefan/7769584/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2Br)C=C1) `REAL300000003760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003760 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 28, 24, 28, 28, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 24, 8, 1, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003760 none O=C([O-])C1=CC=C(NN=CC2=CC=C(Br)C=C2Br)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 17, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 22, 28, 28, 28, 1, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003760 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003760 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003760/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003760 Building REAL300000003761 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003761' /scratch/stefan/7769584/working/building/REAL300000003761 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003761 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003761/0 /scratch/stefan/7769584/working/building/REAL300000003761 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/870 `/scratch/stefan/7769584/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2F)C=C1) `REAL300000003761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003761 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 17, 1, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 23, 27, 27, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 28, 23, 6, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003761 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC(F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 17, 1, 1, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 23, 28, 28, 1, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003761 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003761 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003761/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003761 Building REAL300000003762 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003762' /scratch/stefan/7769584/working/building/REAL300000003762 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003762 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003762/0 /scratch/stefan/7769584/working/building/REAL300000003762 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/871 `/scratch/stefan/7769584/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=CN=C1) `REAL300000003762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003762 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=CN=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 13, 13, 11, 11, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1] 13 rigid atoms, others: [37, 38, 39, 40, 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]) total number of confs: 35 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003762 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=CN=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13] 13 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 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: 31 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003762 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=CN=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 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, 6, 6, 7, 7, 6, 6, 7, 6, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 7, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3] 13 rigid atoms, others: [0, 1, 2, 3, 4, 34, 15, 16, 17, 35, 36, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 32 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003762 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003762 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003762/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003762 Building REAL300000003763 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003763' /scratch/stefan/7769584/working/building/REAL300000003763 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003763 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003763/0 /scratch/stefan/7769584/working/building/REAL300000003763 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/872 `/scratch/stefan/7769584/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C(Br)C=C1) `REAL300000003763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003763 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C(Br)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1] 6 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 10 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003763 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C(Br)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 14 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: REAL300000003763 none CC1(C)C(N=NC2=CC=C(C(=O)[O-])C=C2)CC1C1=CC=C(Br)C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 6, 6, 1, 1, 1, 2, 2, 2, 2] 6 rigid atoms, others: [0, 1, 2, 3, 4, 37, 15, 16, 17, 35, 36, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 24 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003763 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003763 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003763/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003763 Building REAL300000003764 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003764' /scratch/stefan/7769584/working/building/REAL300000003764 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003764 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003764/0 /scratch/stefan/7769584/working/building/REAL300000003764 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/873 `/scratch/stefan/7769584/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2F)C=C1) `REAL300000003764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003764 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 16, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 23, 21, 23, 23, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 21, 7, 1, 1, 23, 23] 23 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000003764 none O=C([O-])C1=CC=C(NN=CC2=CC(Cl)=C(Br)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 16, 1, 17, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 21, 21, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 10, 21, 23, 23, 1, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003764 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003764 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003764/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003764 Building REAL300000003765 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003765' /scratch/stefan/7769584/working/building/REAL300000003765 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003765 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003765/0 /scratch/stefan/7769584/working/building/REAL300000003765 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/874 `/scratch/stefan/7769584/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC([N+](=O)[O-])=C2)C=C1) `REAL300000003765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003765 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 39, 49, 49, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 33, 9, 1, 1, 1, 49, 49] 49 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003765 none O=C([O-])C1=CC=C(NN=CC2=CC(Br)=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 10, 32, 49, 49, 49, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003765 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003765 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003765/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003765 Building REAL300000003766 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003766' /scratch/stefan/7769584/working/building/REAL300000003766 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003766 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003766/0 /scratch/stefan/7769584/working/building/REAL300000003766 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/875 `/scratch/stefan/7769584/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC(Br)=C1F) `REAL300000003766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003766 none COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC(Br)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 29, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 42, 42, 42, 28, 6, 1, 1, 1, 1, 40, 40] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003766 none COC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC(Br)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 10, 10, 30, 40, 40, 30, 30, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 30, 40, 40, 40, 40, 1, 1] 42 rigid atoms, others: [32, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003766 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003766 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003766/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003766 Building REAL300000003767 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003767' /scratch/stefan/7769584/working/building/REAL300000003767 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003767 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003767/0 /scratch/stefan/7769584/working/building/REAL300000003767 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/876 `/scratch/stefan/7769584/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003767 none CC(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 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: [83, 83, 83, 83, 83, 83, 83, 94, 94, 94, 83, 36, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 94, 94, 94, 94, 94, 94, 94, 94, 94, 83, 35, 6, 1, 1, 1, 1] 94 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003767 none CC(C)C1=NN(C(C)(C)C)C=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 13, 13, 55, 83, 83, 55, 57, 83, 83, 83, 83, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 13, 55, 83, 83, 83, 83] 94 rigid atoms, others: [1, 3, 4, 5, 6, 40, 10, 11, 12] set([0, 2, 7, 8, 9, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 354 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003767 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003767 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003767/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003767 Building REAL300000003768 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003768' /scratch/stefan/7769584/working/building/REAL300000003768 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003768 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003768/0 /scratch/stefan/7769584/working/building/REAL300000003768 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/877 `/scratch/stefan/7769584/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)F)=C2F)C=C1) `REAL300000003768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003768 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 27, 27, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 23, 8, 1, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003768 none O=C([O-])C1=CC=C(NN=CC2=CC=CC(C(F)(F)F)=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 21, 21, 26, 26, 24, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 9, 21, 26, 26, 26, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003768 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003768 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003768/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003768 Building REAL300000003769 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003769' /scratch/stefan/7769584/working/building/REAL300000003769 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003769 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003769/0 /scratch/stefan/7769584/working/building/REAL300000003769 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/878 `/scratch/stefan/7769584/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=N3)C=C2)C=C1) `REAL300000003769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003769 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 23, 31, 31, 23, 11, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 31, 31, 31, 31, 22, 10, 3, 3, 1, 1, 3, 3, 31, 31] 31 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003769 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 12, 16, 16, 12, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 16, 16, 16, 16, 11, 5, 1, 1, 3, 2, 1, 1, 16, 16] 31 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003769 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3C=CN=N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 14, 14, 16, 16, 16, 16, 31, 31, 31, 31, 16, 16, 1, 1, 1, 1, 8, 14, 16, 16, 31, 31, 16, 16, 1, 1] 31 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 21, 22, 23, 24, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003769 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003769 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003769/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003769 Building REAL300000003770 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003770' /scratch/stefan/7769584/working/building/REAL300000003770 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003770 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003770/0 /scratch/stefan/7769584/working/building/REAL300000003770 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/879 `/scratch/stefan/7769584/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC2=CC=CC=C12) `REAL300000003770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003770 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 23, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 23, 7, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003770 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C=CC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 34, 40, 40, 34, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 34, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 37] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003770 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003770 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003770/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003770 Building REAL300000003771 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003771' /scratch/stefan/7769584/working/building/REAL300000003771 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003771 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003771/0 /scratch/stefan/7769584/working/building/REAL300000003771 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/880 `/scratch/stefan/7769584/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3C(Br)=C2)C=C1) `REAL300000003771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003771 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3C(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 34, 10, 1, 1, 1, 1, 1, 1, 41, 41] 41 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 21, 22, 23, 24, 25, 26]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003771 none O=C([O-])C1=CC=C(NN=CC2=CC3=CC=CC=C3C(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 10, 22, 41, 41, 41, 41, 41, 41, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003771 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003771 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003771/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003771 Building REAL300000003772 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003772' /scratch/stefan/7769584/working/building/REAL300000003772 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003772 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003772/0 /scratch/stefan/7769584/working/building/REAL300000003772 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/881 `/scratch/stefan/7769584/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2C=CNC2=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003772 none COC1=C2C=CNC2=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 30, 30, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 30, 7, 1, 1, 1, 1] 42 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000003772 none COC1=C2C=CNC2=CC=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 31, 42, 42, 38, 42, 42, 42, 42, 42, 5, 5, 5, 1, 1, 1, 1, 1, 11, 31, 42, 42, 42, 42] 42 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30] set([0, 32, 34, 35, 36, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/7769584/working/building/REAL300000003772 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003772 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003772/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003772 Building REAL300000003773 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003773' /scratch/stefan/7769584/working/building/REAL300000003773 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003773 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003773/0 /scratch/stefan/7769584/working/building/REAL300000003773 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/882 `/scratch/stefan/7769584/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1) `REAL300000003773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003773 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 52, 66, 66, 52, 21, 21, 4, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 66, 66, 66, 66, 52, 21, 5, 5, 1, 1, 1, 1, 1, 6, 1, 1, 5, 5, 66, 66] 198 rigid atoms, others: [32, 33, 34, 36, 37, 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, 38, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003773 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 18, 23, 23, 18, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 23, 23, 23, 23, 18, 6, 1, 1, 5, 5, 5, 5, 5, 15, 5, 5, 1, 1, 23, 23] 198 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003773 none O=C([O-])C1=CC=C(NN=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 21, 21, 24, 24, 21, 22, 66, 66, 66, 66, 66, 24, 24, 1, 1, 1, 1, 8, 21, 24, 24, 66, 66, 66, 66, 66, 198, 66, 66, 24, 24, 1, 1] 198 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003773 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003773/1 /scratch/stefan/7769584/working/building/REAL300000003773 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/883 `/scratch/stefan/7769584/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N[NH+]=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1) `REAL300000003773.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003773 none O=C([O-])C1=CC=C(N[NH+]=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 68, 44, 13, 13, 13, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 68, 68, 68, 68, 44, 13, 5, 5, 1, 1, 1, 1, 1, 6, 1, 1, 5, 5, 68, 68] 204 rigid atoms, others: [32, 33, 34, 35, 37, 38, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003773 none O=C([O-])C1=CC=C(N[NH+]=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 20, 20, 20, 20, 14, 4, 1, 1, 5, 5, 5, 5, 5, 15, 5, 5, 1, 1, 20, 20] 204 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 64 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: REAL300000003773 none O=C([O-])C1=CC=C(N[NH+]=CC2=CC=C(N3CCC(O)C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 8, 8, 8, 20, 20, 20, 20, 68, 68, 68, 68, 68, 20, 20, 1, 1, 1, 1, 7, 8, 20, 20, 68, 68, 68, 68, 68, 204, 68, 68, 20, 20, 1, 1] 204 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 311 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003773 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003773 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003773/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003773/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003773 Building REAL300000003774 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003774' /scratch/stefan/7769584/working/building/REAL300000003774 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003774 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003774/0 /scratch/stefan/7769584/working/building/REAL300000003774 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/884 `/scratch/stefan/7769584/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=C(Br)C=N3)C=C2)C=C1) `REAL300000003774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003774 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=C(Br)C=N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 180, 75, 75, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 180, 75, 35, 35, 9, 9, 1, 1, 35, 35, 201, 201] 201 rigid atoms, others: [33, 34, 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, 35, 36, 37, 38]) total number of confs: 530 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003774 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=C(Br)C=N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 31, 56, 56, 30, 4, 4, 1, 1, 1, 1, 1, 1, 7, 35, 35, 35, 35, 35, 1, 1, 56, 56, 56, 56, 30, 4, 1, 1, 7, 7, 35, 35, 1, 1, 56, 56] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 37, 38]) 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: REAL300000003774 none O=C([O-])C1=CC=C(NN=CC2=CC=C(CN3C=C(Br)C=N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 17, 1, 8, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 30, 30, 56, 56, 56, 56, 143, 201, 201, 201, 201, 201, 56, 56, 1, 1, 1, 1, 9, 30, 56, 56, 143, 143, 201, 201, 56, 56, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003774 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003774 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003774/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003774 Building REAL300000003775 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003775' /scratch/stefan/7769584/working/building/REAL300000003775 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003775 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003775/0 /scratch/stefan/7769584/working/building/REAL300000003775 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/885 `/scratch/stefan/7769584/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(OC)=C1C=NNC1=CC=C(C(=O)[O-])C=C1) `REAL300000003775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003775 none COC1=CC=C(OC)C(OC)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [115, 101, 101, 101, 100, 101, 101, 147, 101, 101, 151, 31, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 101, 101, 147, 147, 147, 151, 151, 151, 30, 6, 1, 1, 1, 1] 153 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003775 none COC1=CC=C(OC)C(OC)=C1C=NNC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 1, 1, 6, 1, 1, 12, 12, 57, 101, 101, 73, 101, 101, 101, 101, 101, 3, 3, 3, 1, 1, 3, 3, 3, 7, 7, 7, 12, 57, 101, 101, 101, 101] 153 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 27, 28] set([0, 7, 10, 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]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003775 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003775/1 /scratch/stefan/7769584/working/building/REAL300000003775 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/886 `/scratch/stefan/7769584/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(OC)=C1CN=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003775.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003775 none COC1=CC=C(OC)C(OC)=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [108, 84, 84, 84, 84, 84, 84, 128, 83, 83, 122, 31, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 84, 84, 128, 128, 128, 122, 122, 122, 31, 31, 1, 1, 1, 1] 130 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 369 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: REAL300000003775 none COC1=CC=C(OC)C(OC)=C1CN=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 1, 1, 5, 1, 1, 6, 50, 50, 83, 83, 50, 50, 83, 83, 83, 83, 3, 3, 3, 1, 1, 4, 4, 4, 5, 5, 5, 6, 6, 83, 83, 83, 83] 130 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 27, 28] set([0, 7, 10, 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]) total number of confs: 348 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003775 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003775 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003775/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003775/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003775 Building REAL300000003776 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003776' /scratch/stefan/7769584/working/building/REAL300000003776 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003776 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003776/0 /scratch/stefan/7769584/working/building/REAL300000003776 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/887 `/scratch/stefan/7769584/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)C=C1) `REAL300000003776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003776 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 49, 49, 37, 21, 21, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 37, 21, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 49 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45]) total number of confs: 193 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003776 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 32, 16, 32, 32, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 32, 32, 32, 32, 16, 4, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 32, 32] 49 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003776 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2C(=O)N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 36, 36, 60, 60, 60, 60, 60, 60, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 10, 36, 60, 60, 60, 60, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003776 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003776 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003776/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003776 Building REAL300000003777 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003777' /scratch/stefan/7769584/working/building/REAL300000003777 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003777 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003777/0 /scratch/stefan/7769584/working/building/REAL300000003777 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/888 `/scratch/stefan/7769584/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)C=C1) `REAL300000003777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003777 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need 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, 201, 201, 200, 126, 126, 97, 97, 97, 97, 97, 97, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 126, 97, 97, 97, 97, 8, 8, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003777 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens 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, 22, 32, 22, 32, 32, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 97, 97, 48, 97, 97, 97, 32, 32, 32, 32, 22, 5, 1, 1, 1, 1, 29, 29, 97, 97, 97, 97, 32, 32] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003777 none O=C([O-])C1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 20, 20, 35, 35, 35, 35, 35, 35, 72, 156, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 20, 35, 35, 35, 35, 156, 156, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003777 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003777 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003777/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003777 Building REAL300000003778 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003778' /scratch/stefan/7769584/working/building/REAL300000003778 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003778 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003778/0 /scratch/stefan/7769584/working/building/REAL300000003778 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/889 `/scratch/stefan/7769584/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=NC=CC=C2C=C1) `REAL300000003778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003778 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 26, 26, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 26, 7, 1, 1, 1, 1, 43, 43, 43, 43, 43] 43 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) 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: REAL300000003778 none CC1=C(C=NNC2=CC=C(C(=O)[O-])C=C2)C2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 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, 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 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, 9, 9, 35, 43, 43, 38, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 35, 43, 43, 43, 43, 1, 1, 1, 1, 1] 43 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003778 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003778 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003778/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003778 Building REAL300000003779 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003779' /scratch/stefan/7769584/working/building/REAL300000003779 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003779 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003779/0 /scratch/stefan/7769584/working/building/REAL300000003779 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/890 `/scratch/stefan/7769584/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CN=C1N1C=CC=N1) `REAL300000003779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003779 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CN=C1N1C=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 8, 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, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 29, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 29, 37, 37, 37, 37, 4, 1, 1, 1] 37 rigid atoms, others: [35, 36, 37, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003779 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CN=C1N1C=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 8, 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, 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 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, 22, 22, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 22, 7, 1, 1, 1, 1, 37, 37, 37, 37] 37 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 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: REAL300000003779 none CC1=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=CN=C1N1C=CC=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 8, 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, 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 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, 10, 10, 28, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 4, 4, 4, 4, 2, 2, 2, 1, 10, 28, 37, 37, 37, 37, 1, 4, 4, 4] 37 rigid atoms, others: [0, 1, 2, 3, 4, 34, 16, 17, 18, 19, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003779 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003779 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003779/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003779 Building REAL300000003780 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003780' /scratch/stefan/7769584/working/building/REAL300000003780 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003780 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003780/0 /scratch/stefan/7769584/working/building/REAL300000003780 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/891 `/scratch/stefan/7769584/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003780 none COC(=O)C1=CN(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 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: [152, 152, 107, 152, 107, 107, 107, 107, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 152, 152, 152, 107, 107, 107, 107, 37, 6, 1, 1, 1, 1, 107] 152 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003780 none COC(=O)C1=CN(C)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 66, 107, 107, 67, 67, 107, 107, 107, 107, 1, 13, 13, 13, 1, 2, 2, 2, 12, 66, 107, 107, 107, 107, 1] 152 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 21, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003780 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003780 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003780/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003780 Building REAL300000003781 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003781' /scratch/stefan/7769584/working/building/REAL300000003781 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003781 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003781/0 /scratch/stefan/7769584/working/building/REAL300000003781 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/892 `/scratch/stefan/7769584/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(NN=CC2=CC3=C(C=C(Cl)S3)N2)C=C1) `REAL300000003781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003781 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(C=C(Cl)S3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 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, 18, 24, 24, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 18, 7, 1, 1, 1, 24, 24] 24 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 28, 29]) 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: REAL300000003781 none O=C([O-])C1=CC=C(NN=CC2=CC3=C(C=C(Cl)S3)N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 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 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, 10, 18, 18, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 10, 18, 24, 24, 24, 1, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003781 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003781 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003781/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003781 Building REAL300000003782 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003782' /scratch/stefan/7769584/working/building/REAL300000003782 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003782 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003782/0 /scratch/stefan/7769584/working/building/REAL300000003782 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/893 `/scratch/stefan/7769584/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C(C)N=NC3=CC=C(C(=O)[O-])C=C3)N=CC=C2C=C1) `REAL300000003782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003782 none COC1=CC2=C(C(C)N=NC3=CC=C(C(=O)[O-])C=C3)N=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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 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, 21, 5, 21, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 21, 21, 1, 1, 1, 1, 40, 40, 40, 40] 40 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 98 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: REAL300000003782 none COC1=CC2=C(C(C)N=NC3=CC=C(C(=O)[O-])C=C3)N=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.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, 5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 27, 27, 40, 40, 27, 27, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 40, 40, 40, 40, 1, 1, 1, 1] 40 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22, 23, 24, 38, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003782 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003782/1 /scratch/stefan/7769584/working/building/REAL300000003782 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/894 `/scratch/stefan/7769584/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C(C)=NNC3=CC=C(C(=O)[O-])C=C3)N=CC=C2C=C1) `REAL300000003782.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003782 none COC1=CC2=C(C(C)=NNC3=CC=C(C(=O)[O-])C=C3)N=CC=C2C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 32, 31, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 32, 32, 32, 5, 1, 1, 1, 1, 77, 77, 77, 77] 77 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 118 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: REAL300000003782 none COC1=CC2=C(C(C)=NNC3=CC=C(C(=O)[O-])C=C3)N=CC=C2C=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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 43, 77, 77, 43, 54, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 10, 10, 43, 77, 77, 77, 77, 1, 1, 1, 1] 77 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22, 23, 24, 38, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 326 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003782 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003782 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003782/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003782/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003782 Building REAL300000003783 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003783' /scratch/stefan/7769584/working/building/REAL300000003783 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003783 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003783/0 /scratch/stefan/7769584/working/building/REAL300000003783 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/895 `/scratch/stefan/7769584/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)N2C=C1) `REAL300000003783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003783 none COC1=CC2=NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)N2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 85, 46, 46, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 46, 7, 1, 1, 1, 1, 85, 85] 85 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003783 none COC1=CC2=NC=C(C=NNC3=CC=C(C(=O)[O-])C=C3)N2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 85, 85, 53, 71, 85, 85, 85, 85, 1, 1, 1, 3, 3, 3, 1, 1, 10, 51, 85, 85, 85, 85, 1, 1] 85 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003783 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003783 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003783/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003783 Building REAL300000003784 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003784' /scratch/stefan/7769584/working/building/REAL300000003784 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003784 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003784/0 /scratch/stefan/7769584/working/building/REAL300000003784 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/896 `/scratch/stefan/7769584/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1O) `REAL300000003784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003784 none COC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1O 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 92, 92, 92, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92, 37, 6, 1, 1, 1, 1, 184] 184 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 311 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003784 none COC1=CC=C(Br)C(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1O 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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 68, 92, 92, 82, 92, 92, 92, 92, 92, 1, 1, 3, 3, 3, 1, 1, 12, 68, 92, 92, 92, 92, 2] 184 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003784 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003784 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003784/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003784 Building REAL300000003785 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003785' /scratch/stefan/7769584/working/building/REAL300000003785 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003785 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003785/0 /scratch/stefan/7769584/working/building/REAL300000003785 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/897 `/scratch/stefan/7769584/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)C=C1) `REAL300000003785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003785 none O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 200, 200, 107, 107, 107, 55, 16, 3, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 201, 201, 201, 201, 107, 107, 107, 107, 55, 55, 3, 3, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 516 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003785 none O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 16, 9, 17, 17, 9, 9, 1, 1, 1, 1, 1, 6, 20, 63, 107, 107, 72, 107, 107, 1, 1, 1, 1, 17, 17, 17, 17, 1, 1, 1, 1, 6, 6, 63, 63, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 45, 46, 44, 42, 21, 22, 23, 24, 47, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49]) 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: REAL300000003785 none O=C([O-])C1=CC=C(N=NC2CC(COCC3=CC=CC=C3)C23CCC3)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', '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.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 19, 19, 19, 47, 117, 201, 201, 201, 201, 201, 201, 19, 19, 19, 19, 1, 1, 1, 1, 19, 19, 19, 19, 47, 47, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 48, 49, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003785 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003785 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003785/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003785 Building REAL300000003786 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003786' /scratch/stefan/7769584/working/building/REAL300000003786 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003786 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003786/0 /scratch/stefan/7769584/working/building/REAL300000003786 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/898 `/scratch/stefan/7769584/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Br)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000003786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003786 none COC(=O)C1=CC(Br)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 4, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 90, 170, 90, 90, 90, 90, 90, 34, 34, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 90, 170, 170, 170, 90, 90, 34, 7, 1, 1, 1, 1, 90] 170 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003786 none COC(=O)C1=CC(Br)=CC(C=NNC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 4, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 58, 90, 90, 59, 59, 90, 90, 90, 90, 1, 13, 13, 13, 1, 1, 12, 58, 90, 90, 90, 90, 1] 170 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 34, 22, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003786 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003786 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003786/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003786 Building REAL300000003787 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003787' /scratch/stefan/7769584/working/building/REAL300000003787 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003787 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003787/0 /scratch/stefan/7769584/working/building/REAL300000003787 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/899 `/scratch/stefan/7769584/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=CS1) `REAL300000003787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003787 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 40, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 2, 2, 2, 1, 1, 12, 12, 12, 40, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 13, 14, 15, 16, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 123 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003787 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 47, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 7, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003787 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003787/1 /scratch/stefan/7769584/working/building/REAL300000003787 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/900 `/scratch/stefan/7769584/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=CS1) `REAL300000003787.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003787 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [13, 1, 13, 55, 55, 56, 56, 55, 55, 56, 56, 56, 56, 1, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13, 13, 56, 56, 56, 56, 1, 1] 56 rigid atoms, others: [1, 13, 14, 15, 16, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 22, 23, 24, 25, 26, 27, 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: REAL300000003787 none CC(N=NC1=CC=C(C(=O)[O-])C=C1)C1=CC(C(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 56, 56, 56, 56, 56, 56, 56, 56, 22, 22, 22, 22, 1, 1, 1, 1, 56, 56] 56 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003787 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003787 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003787/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003787/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003787 Building REAL300000003788 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003788' /scratch/stefan/7769584/working/building/REAL300000003788 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003788 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003788/0 /scratch/stefan/7769584/working/building/REAL300000003788 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/901 `/scratch/stefan/7769584/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC(F)=C1Br)N=NC1=CC=C(C(=O)[O-])C=C1) `REAL300000003788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003788 none CC(CC1=CC=CC(F)=C1Br)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 21, 36, 53, 53, 53, 53, 53, 53, 53, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 36, 36, 53, 53, 53, 1, 1, 1, 1] 53 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]) 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: REAL300000003788 none CC(CC1=CC=CC(F)=C1Br)N=NC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 50, 50, 53, 53, 50, 51, 53, 53, 53, 53, 16, 16, 16, 16, 8, 8, 1, 1, 1, 53, 53, 53, 53] 53 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]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003788 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003788 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003788/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003788 Building REAL300000003789 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003789' /scratch/stefan/7769584/working/building/REAL300000003789 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003789 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003789/0 /scratch/stefan/7769584/working/building/REAL300000003789 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/902 `/scratch/stefan/7769584/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)C=C1F) `REAL300000003789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003789 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 2, 2, 7, 7, 7, 7, 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: [11, 1, 11, 11, 38, 49, 49, 48, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 11, 38, 49, 49, 49, 49, 1, 1, 1] 49 rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 128 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003789 none CC(=NNC1=CC=C(C(=O)[O-])C=C1)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 2, 2, 7, 7, 7, 7, 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: [25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 49, 49, 45, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 6, 1, 1, 1, 1, 49, 49, 49] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003789 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003789 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003789/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003789 Building REAL300000003790 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003790' /scratch/stefan/7769584/working/building/REAL300000003790 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003790 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003790/0 /scratch/stefan/7769584/working/building/REAL300000003790 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/903 `/scratch/stefan/7769584/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)C([N+](=O)[O-])=C1) `REAL300000003790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003790 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 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: [117, 33, 118, 117, 33, 65, 65, 33, 33, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 118, 118, 65, 65, 5, 5, 1, 1, 1, 1, 65] 135 rigid atoms, others: [32, 33, 34, 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, 35]) 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: REAL300000003790 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 26, 65, 65, 36, 64, 65, 65, 65, 65, 1, 1, 2, 2, 1, 5, 5, 1, 1, 25, 26, 65, 65, 65, 65, 1] 135 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 20, 21, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003790 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003790 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003790/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003790 Building REAL300000003791 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003791' /scratch/stefan/7769584/working/building/REAL300000003791 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003791 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003791/0 /scratch/stefan/7769584/working/building/REAL300000003791 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/904 `/scratch/stefan/7769584/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])C([N+](=O)[O-])=C1) `REAL300000003791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003791 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 29, 57, 57, 29, 31, 31, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 52, 52, 31, 31, 31, 31, 31, 57, 57, 31, 31, 7, 7, 1, 1, 1, 1, 29, 29, 31] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) 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: REAL300000003791 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 3, 3, 11, 31, 31, 28, 31, 31, 31, 83, 149, 151, 151, 1, 1, 2, 2, 1, 5, 5, 1, 1, 11, 11, 31, 31, 30, 31, 149, 149, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 22, 23, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003791 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003791 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003791/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003791 Building REAL300000003792 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003792' /scratch/stefan/7769584/working/building/REAL300000003792 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003792 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003792/0 /scratch/stefan/7769584/working/building/REAL300000003792 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/905 `/scratch/stefan/7769584/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)C([N+](=O)[O-])=C1) `REAL300000003792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003792 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [50, 20, 50, 50, 20, 21, 21, 20, 20, 4, 1, 1, 1, 1, 1, 1, 6, 17, 28, 28, 1, 1, 21, 21, 21, 21, 21, 50, 50, 21, 21, 4, 4, 1, 1, 17, 17, 1, 1, 21] 201 rigid atoms, others: [33, 34, 37, 38, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39]) 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: REAL300000003792 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 3, 3, 9, 21, 21, 9, 9, 74, 139, 156, 156, 21, 21, 1, 1, 2, 2, 1, 5, 5, 1, 1, 8, 9, 21, 21, 139, 139, 21, 21, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 22, 23, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003792 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003792 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003792/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003792 Building REAL300000003793 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003793' /scratch/stefan/7769584/working/building/REAL300000003793 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003793 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003793/0 /scratch/stefan/7769584/working/building/REAL300000003793 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/906 `/scratch/stefan/7769584/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])C([N+](=O)[O-])=C1) `REAL300000003793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003793 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 53, 173, 173, 52, 99, 99, 52, 51, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 99, 99, 99, 99, 99, 173, 173, 99, 99, 8, 8, 1, 1, 1, 1, 99] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 795 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003793 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 38, 99, 99, 98, 99, 99, 99, 117, 117, 1, 1, 2, 2, 1, 5, 5, 1, 1, 38, 38, 99, 99, 99, 99, 1] 201 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 20, 21, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003793 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003793 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003793/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003793 Building REAL300000003794 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003794' /scratch/stefan/7769584/working/building/REAL300000003794 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003794 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003794/0 /scratch/stefan/7769584/working/building/REAL300000003794 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/907 `/scratch/stefan/7769584/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1) `REAL300000003794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003794 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 38, 38, 47, 47, 38, 38, 94, 94, 94, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 47, 47, 94, 94, 47, 1, 1, 1, 1] 98 rigid atoms, others: [1, 35, 36, 37, 38, 17, 18, 19, 20, 21, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000003794 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 20, 47, 47, 20, 27, 47, 47, 47, 47, 20, 20, 20, 20, 1, 1, 5, 5, 1, 47, 47, 47, 47] 98 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 14, 30, 31] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003794 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003794 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003794/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003794 Building REAL300000003795 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003795' /scratch/stefan/7769584/working/building/REAL300000003795 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003795 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003795/0 /scratch/stefan/7769584/working/building/REAL300000003795 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/908 `/scratch/stefan/7769584/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(CC(=O)[O-])C=C1) `REAL300000003795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003795 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 36, 36, 53, 53, 36, 36, 134, 134, 134, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 7, 7, 53, 53, 134, 134, 53, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [1, 36, 37, 40, 41, 17, 18, 19, 20, 21, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 540 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003795 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 23, 53, 53, 24, 36, 72, 78, 78, 53, 53, 23, 23, 23, 23, 1, 1, 5, 5, 1, 53, 53, 72, 72, 53, 53] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 14, 35, 31] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003795 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003795 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003795/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003795 Building REAL300000003796 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003796' /scratch/stefan/7769584/working/building/REAL300000003796 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003796 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003796/0 /scratch/stefan/7769584/working/building/REAL300000003796 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/909 `/scratch/stefan/7769584/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)C([N+](=O)[O-])=C1) `REAL300000003796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003796 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 28, 55, 54, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 7, 16, 28, 28, 1, 28, 28, 29, 29, 28, 55, 55, 28, 28, 6, 6, 1, 1, 1, 16, 16, 1, 28] 201 rigid atoms, others: [33, 34, 35, 38, 10, 11, 12, 13, 14, 15, 16, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 39]) total number of confs: 262 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: REAL300000003796 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 28, 28, 99, 144, 155, 155, 28, 1, 1, 2, 2, 1, 4, 4, 1, 1, 7, 7, 28, 28, 28, 144, 144, 28, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 39, 22, 23, 26, 29, 30] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 437 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003796 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003796 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003796/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003796 Building REAL300000003797 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003797' /scratch/stefan/7769584/working/building/REAL300000003797 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003797 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003797/0 /scratch/stefan/7769584/working/building/REAL300000003797 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/910 `/scratch/stefan/7769584/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)C([N+](=O)[O-])=C1) `REAL300000003797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003797 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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: [179, 63, 179, 179, 63, 116, 116, 63, 63, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 116, 116, 116, 116, 116, 179, 179, 116, 116, 9, 9, 1, 1, 1, 116] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 854 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003797 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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, 4, 4, 1, 1, 1, 1, 1, 5, 5, 30, 116, 116, 116, 116, 116, 116, 116, 1, 1, 2, 2, 1, 5, 5, 1, 1, 30, 30, 116, 116, 116, 1] 201 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 19, 20, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003797 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003797 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003797/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003797 Building REAL300000003798 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003798' /scratch/stefan/7769584/working/building/REAL300000003798 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003798 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003798/0 /scratch/stefan/7769584/working/building/REAL300000003798 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/911 `/scratch/stefan/7769584/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1) `REAL300000003798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003798 none CCC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 7, 1, 7, 35, 35, 53, 53, 35, 35, 125, 125, 125, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 7, 53, 53, 125, 125, 53, 1, 1, 1, 1] 135 rigid atoms, others: [2, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000003798 none CCC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 25, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 25, 53, 53, 37, 41, 53, 53, 53, 53, 39, 39, 39, 39, 39, 25, 1, 1, 5, 5, 1, 53, 53, 53, 53] 135 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 13, 14, 15, 37] set([0, 1, 2, 3, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40, 41]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003798 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003798 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003798/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003798 Building REAL300000003799 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003799' /scratch/stefan/7769584/working/building/REAL300000003799 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003799 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003799/0 /scratch/stefan/7769584/working/building/REAL300000003799 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/912 `/scratch/stefan/7769584/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=CC=C1C(=O)[O-]) `REAL300000003799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003799 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 31, 31, 51, 51, 31, 31, 110, 110, 110, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 51, 51, 110, 110, 51, 1, 1, 1, 1] 129 rigid atoms, others: [1, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 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]) 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: REAL300000003799 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [34, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 34, 51, 51, 51, 51, 51, 51, 51, 51, 34, 34, 34, 34, 1, 1, 5, 5, 1, 51, 51, 51, 51] 129 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 14, 30, 31] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003799 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003799 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003799/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003799 Building REAL300000003800 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003800' /scratch/stefan/7769584/working/building/REAL300000003800 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003800 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003800/0 /scratch/stefan/7769584/working/building/REAL300000003800 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/913 `/scratch/stefan/7769584/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CC=C1O) `REAL300000003800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003800 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 42, 42, 60, 60, 42, 42, 110, 110, 110, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 60, 60, 110, 110, 60, 1, 1, 1, 2] 234 rigid atoms, others: [1, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 437 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003800 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [29, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 29, 60, 60, 60, 60, 60, 60, 60, 60, 60, 29, 29, 29, 29, 1, 1, 5, 5, 1, 60, 60, 60, 120] 234 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 14, 35, 31] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39]) total number of confs: 277 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003800 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003800 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003800/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003800 Building REAL300000003801 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003801' /scratch/stefan/7769584/working/building/REAL300000003801 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003801 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003801/0 /scratch/stefan/7769584/working/building/REAL300000003801 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/914 `/scratch/stefan/7769584/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=CC(C(=O)[O-])=C1) `REAL300000003801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003801 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 71, 71, 108, 108, 108, 108, 201, 201, 201, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 108, 108, 201, 201, 108, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000003801 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 32, 108, 108, 108, 108, 108, 108, 108, 108, 32, 32, 32, 32, 1, 1, 5, 5, 1, 108, 108, 108, 108] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 14, 30, 31] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003801 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003801 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003801/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003801 Building REAL300000003802 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003802' /scratch/stefan/7769584/working/building/REAL300000003802 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003802 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003802/0 /scratch/stefan/7769584/working/building/REAL300000003802 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/915 `/scratch/stefan/7769584/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)C([N+](=O)[O-])=C1) `REAL300000003802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003802 none NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 49, 142, 142, 49, 57, 57, 49, 49, 9, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 57, 57, 57, 57, 57, 142, 142, 57, 57, 9, 9, 1, 6, 6, 57] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) 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: REAL300000003802 none NS(=O)(=O)C1=CC=C(N=NCC2=CN(CC(=O)[O-])N=N2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 3, 3, 17, 57, 57, 57, 103, 113, 113, 57, 57, 1, 1, 2, 2, 1, 5, 5, 1, 1, 17, 17, 57, 103, 103, 1] 201 rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 20, 21, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003802 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003802 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003802/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003802 Building REAL300000003803 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003803' /scratch/stefan/7769584/working/building/REAL300000003803 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003803 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003803/0 /scratch/stefan/7769584/working/building/REAL300000003803 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/916 `/scratch/stefan/7769584/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000003803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003803 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 73, 73, 104, 104, 73, 94, 201, 201, 201, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 13, 13, 104, 104, 201, 201, 104, 1, 1, 1] 201 rigid atoms, others: [1, 36, 37, 38, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003803 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 26, 104, 104, 104, 104, 111, 111, 104, 104, 104, 26, 26, 26, 26, 1, 1, 5, 5, 1, 104, 104, 104] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 12, 13, 14, 35, 31] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003803 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003803 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003803/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003803 Building REAL300000003804 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003804' /scratch/stefan/7769584/working/building/REAL300000003804 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003804 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003804/0 /scratch/stefan/7769584/working/building/REAL300000003804 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/917 `/scratch/stefan/7769584/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)C([N+](=O)[O-])=C1) `REAL300000003804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003804 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 63, 179, 179, 63, 119, 119, 63, 62, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 179, 179, 119, 119, 8, 8, 1, 1, 119] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) 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: REAL300000003804 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CS2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 14, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 29, 118, 118, 118, 119, 118, 118, 118, 1, 1, 2, 2, 1, 5, 5, 1, 1, 29, 29, 118, 118, 1] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 19, 20, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 28, 29, 30, 31]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003804 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003804 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003804/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003804 Building REAL300000003805 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003805' /scratch/stefan/7769584/working/building/REAL300000003805 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003805 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003805/0 /scratch/stefan/7769584/working/building/REAL300000003805 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/918 `/scratch/stefan/7769584/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)C([N+](=O)[O-])=C1) `REAL300000003805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003805 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 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] 0 hydrogens 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, 54, 170, 170, 54, 94, 94, 54, 53, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 94, 94, 94, 94, 94, 169, 170, 94, 94, 8, 8, 1, 1, 1, 94] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003805 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 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] 0 hydrogens 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, 5, 5, 33, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 2, 2, 1, 5, 5, 1, 1, 33, 33, 94, 94, 94, 1] 201 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003805 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003805 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003805/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003805 Building REAL300000003806 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003806' /scratch/stefan/7769584/working/building/REAL300000003806 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003806 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003806/0 /scratch/stefan/7769584/working/building/REAL300000003806 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/919 `/scratch/stefan/7769584/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)C([N+](=O)[O-])=C1) `REAL300000003806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003806 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [176, 61, 176, 176, 61, 115, 115, 61, 61, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 115, 115, 116, 116, 115, 177, 177, 115, 115, 8, 8, 1, 1, 2, 1, 115] 402 rigid atoms, others: [32, 33, 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, 34, 36]) total number of confs: 841 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003806 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(O)C(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 31, 115, 115, 115, 115, 115, 115, 116, 116, 115, 1, 1, 2, 2, 1, 5, 5, 1, 1, 31, 31, 115, 115, 230, 115, 1] 402 rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003806 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003806/1 /scratch/stefan/7769584/working/building/REAL300000003806 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/920 `/scratch/stefan/7769584/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C([N+](=O)[O-])=C1) `REAL300000003806.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003806 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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, 19, 58, 58, 19, 22, 22, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 22, 58, 58, 22, 22, 19, 8, 1, 1, 2, 1, 22] 116 rigid atoms, others: [32, 33, 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, 34, 36]) 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: REAL300000003806 none NS(=O)(=O)C1=CC=C(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 1, 5, 5, 1, 1, 6, 17, 22, 22, 44, 22, 1] 116 rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003806 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003806 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003806/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003806/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003806 Building REAL300000003807 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003807' /scratch/stefan/7769584/working/building/REAL300000003807 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003807 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003807/0 /scratch/stefan/7769584/working/building/REAL300000003807 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/921 `/scratch/stefan/7769584/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003807 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [51, 51, 51, 51, 51, 51, 51, 51, 51, 31, 6, 31, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 51, 51, 51, 51, 51, 51, 31, 31, 31, 31, 1, 1, 5, 5, 1] 85 rigid atoms, others: [37, 38, 41, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003807 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 51, 51, 25, 25, 76, 76, 76, 51, 51, 51, 51, 51, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 51, 51, 76, 76, 51] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003807 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003807 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003807/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003807 Building REAL300000003808 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003808' /scratch/stefan/7769584/working/building/REAL300000003808 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003808 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003808/0 /scratch/stefan/7769584/working/building/REAL300000003808 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/922 `/scratch/stefan/7769584/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])O1) `REAL300000003808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003808 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [13, 1, 13, 89, 89, 125, 125, 89, 89, 188, 188, 188, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 125, 125, 188, 188, 125, 1, 1] 201 rigid atoms, others: [1, 34, 35, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 758 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003808 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [27, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 27, 125, 125, 125, 125, 125, 125, 125, 27, 27, 27, 27, 1, 1, 5, 5, 1, 125, 125] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 12, 13, 14, 29, 30] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003808 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003808 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003808/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003808 Building REAL300000003809 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003809' /scratch/stefan/7769584/working/building/REAL300000003809 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003809 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003809/0 /scratch/stefan/7769584/working/building/REAL300000003809 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/923 `/scratch/stefan/7769584/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])N1) `REAL300000003809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003809 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 102, 102, 67, 14, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 67, 67, 67, 67, 67, 13, 14, 1, 1, 5, 5, 1, 67] 201 rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003809 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 63, 63, 67, 67, 63, 63, 201, 201, 201, 67, 67, 67, 67, 67, 1, 2, 2, 2, 1, 9, 9, 67, 67, 201, 201, 67, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003809 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003809 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003809/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003809 Building REAL300000003810 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003810' /scratch/stefan/7769584/working/building/REAL300000003810 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003810 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003810/0 /scratch/stefan/7769584/working/building/REAL300000003810 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/924 `/scratch/stefan/7769584/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)C([N+](=O)[O-])=C1) `REAL300000003810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003810 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 11, 44, 44, 11, 19, 19, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 19, 19, 19, 19, 19, 44, 44, 19, 19, 1, 1, 1, 1, 1, 1, 19] 53 rigid atoms, others: [9, 10, 11, 12, 13, 16, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003810 none NS(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 31, 31, 19, 1, 1, 2, 2, 1, 5, 5, 1, 1, 19, 19, 19, 19, 19, 19, 1] 53 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 17, 18, 21, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003810 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003810 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003810/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003810 Building REAL300000003811 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003811' /scratch/stefan/7769584/working/building/REAL300000003811 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003811 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003811/0 /scratch/stefan/7769584/working/building/REAL300000003811 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/925 `/scratch/stefan/7769584/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1) `REAL300000003811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003811 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 98, 200, 200, 62, 119, 119, 62, 62, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 119, 119, 120, 120, 119, 201, 201, 119, 119, 8, 8, 1, 1, 1, 1, 119] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 885 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003811 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 34, 119, 119, 119, 119, 119, 120, 120, 118, 1, 1, 2, 2, 1, 5, 5, 1, 1, 34, 34, 119, 119, 119, 119, 1] 201 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 20, 21, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003811 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003811 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003811/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003811 Building REAL300000003812 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003812' /scratch/stefan/7769584/working/building/REAL300000003812 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003812 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003812/0 /scratch/stefan/7769584/working/building/REAL300000003812 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/926 `/scratch/stefan/7769584/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CSC(C(=O)[O-])=C1) `REAL300000003812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003812 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 80, 80, 126, 126, 126, 126, 201, 201, 201, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 126, 126, 201, 201, 126, 1, 1] 201 rigid atoms, others: [1, 34, 35, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003812 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 30, 126, 126, 126, 126, 126, 126, 126, 30, 30, 30, 30, 1, 1, 5, 5, 1, 126, 126] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 12, 13, 14, 29, 30] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003812 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003812 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003812/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003812 Building REAL300000003813 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003813' /scratch/stefan/7769584/working/building/REAL300000003813 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003813 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003813/0 /scratch/stefan/7769584/working/building/REAL300000003813 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/927 `/scratch/stefan/7769584/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000003813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003813 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 17, 17, 23, 23, 17, 17, 69, 69, 69, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 4, 4, 4, 4, 23, 23, 69, 69, 23, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 101 rigid atoms, others: [1, 38, 39, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003813 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 17, 23, 23, 23, 23, 23, 42, 47, 47, 23, 23, 23, 17, 17, 17, 17, 1, 1, 5, 5, 1, 23, 23, 42, 42, 23, 23, 23, 23, 23, 23] 101 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 12, 13, 14, 37] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003813 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003813 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003813/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003813 Building REAL300000003814 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003814' /scratch/stefan/7769584/working/building/REAL300000003814 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003814 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003814/0 /scratch/stefan/7769584/working/building/REAL300000003814 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/928 `/scratch/stefan/7769584/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003814 none CC(CCCCCCC(=O)[O-])N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 20, 44, 56, 59, 85, 103, 140, 156, 156, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 20, 20, 20, 20, 48, 48, 56, 53, 67, 67, 93, 92, 109, 109, 144, 143, 1, 1, 5, 5, 1] 201 rigid atoms, others: [42, 43, 12, 13, 14, 15, 16, 17, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 889 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003814 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003814 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003814/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003814 Building REAL300000003815 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003815' /scratch/stefan/7769584/working/building/REAL300000003815 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003815 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003815/0 /scratch/stefan/7769584/working/building/REAL300000003815 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/929 `/scratch/stefan/7769584/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003815 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 58, 59, 59, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 27, 27, 27, 27, 27, 58, 58, 27, 27, 27, 27, 27, 1, 1, 5, 5, 1] 128 rigid atoms, others: [37, 38, 41, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) 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: REAL300000003815 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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 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, 10, 14, 14, 1, 1, 1, 1, 12, 12, 27, 27, 12, 12, 61, 61, 61, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 10, 10, 1, 1, 1, 1, 1, 27, 27, 61, 61, 27] 128 rigid atoms, others: [0, 1, 2, 3, 32, 33, 7, 8, 9, 10, 34, 35, 36, 28, 29] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 37, 38, 39, 40, 41]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003815 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003815 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003815/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003815 Building REAL300000003816 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003816' /scratch/stefan/7769584/working/building/REAL300000003816 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003816 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003816/0 /scratch/stefan/7769584/working/building/REAL300000003816 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/930 `/scratch/stefan/7769584/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CS1) `REAL300000003816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003816 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 72, 72, 109, 109, 72, 72, 190, 190, 190, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 109, 109, 190, 190, 109, 1, 1] 201 rigid atoms, others: [1, 34, 35, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 788 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003816 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 28, 109, 109, 109, 109, 109, 109, 109, 28, 28, 28, 28, 1, 1, 5, 5, 1, 109, 109] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 12, 13, 14, 29, 30] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003816 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003816 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003816/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003816 Building REAL300000003817 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003817' /scratch/stefan/7769584/working/building/REAL300000003817 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003817 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003817/0 /scratch/stefan/7769584/working/building/REAL300000003817 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/931 `/scratch/stefan/7769584/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(N=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])CCC(C(=O)[O-])C1(C)C) `REAL300000003817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003817 none CC1C(N=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])CCC(C(=O)[O-])C1(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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 12, 12, 12, 12, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 5, 5, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 27 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 13, 14, 15, 36] set([0, 1, 2, 3, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003817 none CC1C(N=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])CCC(C(=O)[O-])C1(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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 12, 12, 7, 7, 23, 23, 23, 12, 12, 12, 12, 12, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 12, 12, 23, 23, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 24, 25, 26, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003817 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003817 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003817/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003817 Building REAL300000003818 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003818' /scratch/stefan/7769584/working/building/REAL300000003818 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003818 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003818/0 /scratch/stefan/7769584/working/building/REAL300000003818 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/932 `/scratch/stefan/7769584/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003818 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 21, 21, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 5, 5, 1] 33 rigid atoms, others: [37, 38, 41, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) 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: REAL300000003818 none CC1CC(C(=O)[O-])CCC1N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 33, 33, 33, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 33, 33, 12] 33 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 34, 35, 32, 36, 28, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003818 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003818 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003818/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003818 Building REAL300000003819 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003819' /scratch/stefan/7769584/working/building/REAL300000003819 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003819 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003819/0 /scratch/stefan/7769584/working/building/REAL300000003819 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/933 `/scratch/stefan/7769584/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(N=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])CCC1C(=O)[O-]) `REAL300000003819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003819 none CC1CC(N=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])CCC1C(=O)[O-] 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 5, 5, 1, 19, 19, 19, 19, 19] 33 rigid atoms, others: [32, 33, 36, 5, 6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003819 none CC1CC(N=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])CCC1C(=O)[O-] 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 19, 19, 8, 8, 29, 29, 29, 19, 19, 19, 19, 19, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 19, 19, 29, 29, 19, 1, 1, 1, 1, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 19, 20, 21, 22, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003819 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003819 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003819/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003819 Building REAL300000003820 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003820' /scratch/stefan/7769584/working/building/REAL300000003820 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003820 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003820/0 /scratch/stefan/7769584/working/building/REAL300000003820 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/934 `/scratch/stefan/7769584/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1) `REAL300000003820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003820 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 99, 201, 201, 63, 121, 121, 63, 63, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 121, 121, 122, 122, 121, 201, 201, 121, 121, 8, 8, 1, 1, 1, 121] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 925 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003820 none NS(=O)(=O)C1=CC=C(N=NCC2=CNC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 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, 4, 4, 1, 1, 1, 1, 1, 5, 5, 33, 121, 121, 121, 121, 121, 122, 121, 1, 1, 2, 2, 1, 5, 5, 1, 1, 33, 33, 121, 121, 121, 1] 201 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 19, 20, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003820 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003820 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003820/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003820 Building REAL300000003821 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003821' /scratch/stefan/7769584/working/building/REAL300000003821 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003821 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003821/0 /scratch/stefan/7769584/working/building/REAL300000003821 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/935 `/scratch/stefan/7769584/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003821 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 18, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 15, 15, 15, 15, 18, 18, 24, 24, 24, 24, 24, 24, 1, 1, 5, 5, 1] 33 rigid atoms, others: [37, 38, 41, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 105 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: REAL300000003821 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 1, 1, 2, 2, 1, 1, 1, 5, 17, 17, 24, 24, 17, 17, 33, 33, 33, 24, 24, 24, 24, 24, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 24, 24, 33, 33, 24] 33 rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 34, 35, 36, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003821 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003821 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003821/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003821 Building REAL300000003822 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003822' /scratch/stefan/7769584/working/building/REAL300000003822 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003822 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003822/0 /scratch/stefan/7769584/working/building/REAL300000003822 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/936 `/scratch/stefan/7769584/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003822 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 36, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 94, 94, 94, 94, 94, 94, 94, 94, 35, 36, 1, 1, 5, 5, 1] 195 rigid atoms, others: [37, 38, 41, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) 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: REAL300000003822 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 48, 48, 94, 94, 48, 48, 161, 161, 161, 94, 94, 94, 94, 94, 2, 2, 2, 1, 2, 2, 2, 1, 8, 8, 94, 94, 161, 161, 94] 195 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 34, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003822 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003822 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003822/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003822 Building REAL300000003823 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003823' /scratch/stefan/7769584/working/building/REAL300000003823 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003823 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003823/0 /scratch/stefan/7769584/working/building/REAL300000003823 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/937 `/scratch/stefan/7769584/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2Cl)C([N+](=O)[O-])=C1) `REAL300000003823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003823 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 54, 168, 168, 54, 96, 96, 54, 54, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 96, 96, 96, 96, 96, 168, 168, 96, 96, 8, 8, 1, 1, 1, 96] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003823 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(C(=O)[O-])=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 35, 96, 96, 96, 96, 96, 114, 114, 96, 96, 1, 1, 2, 2, 1, 5, 5, 1, 1, 35, 35, 96, 96, 96, 1] 201 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003823 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003823 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003823/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003823 Building REAL300000003824 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003824' /scratch/stefan/7769584/working/building/REAL300000003824 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003824 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003824/0 /scratch/stefan/7769584/working/building/REAL300000003824 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/938 `/scratch/stefan/7769584/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003824 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [74, 74, 74, 74, 74, 74, 90, 90, 36, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 74, 74, 74, 74, 35, 36, 1, 1, 5, 5, 1] 181 rigid atoms, others: [32, 35, 11, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003824 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 47, 48, 74, 74, 48, 48, 165, 165, 165, 74, 74, 74, 74, 74, 2, 2, 2, 1, 8, 8, 74, 74, 165, 165, 74] 181 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 28] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003824 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003824 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003824/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003824 Building REAL300000003825 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003825' /scratch/stefan/7769584/working/building/REAL300000003825 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003825 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003825/0 /scratch/stefan/7769584/working/building/REAL300000003825 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/939 `/scratch/stefan/7769584/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)C([N+](=O)[O-])=C1) `REAL300000003825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003825 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 63, 201, 201, 63, 67, 67, 63, 63, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 67, 67, 67, 67, 67, 201, 201, 67, 67, 9, 9, 1, 1, 1, 67] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003825 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(F)=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 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] 0 hydrogens 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, 3, 3, 11, 67, 67, 66, 66, 105, 105, 67, 67, 67, 1, 1, 2, 2, 1, 5, 5, 1, 1, 11, 11, 67, 67, 67, 1] 201 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003825 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003825 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003825/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003825 Building REAL300000003826 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003826' /scratch/stefan/7769584/working/building/REAL300000003826 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003826 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003826/0 /scratch/stefan/7769584/working/building/REAL300000003826 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/940 `/scratch/stefan/7769584/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)C([N+](=O)[O-])=C1) `REAL300000003826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003826 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 51, 139, 139, 51, 51, 51, 51, 51, 9, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 1, 51, 51, 51, 51, 51, 139, 139, 51, 51, 9, 9, 1, 1, 6, 6, 51] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003826 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C=CC(=O)[O-])O2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 51, 109, 109, 132, 132, 51, 1, 1, 2, 2, 1, 5, 5, 1, 1, 9, 9, 51, 51, 109, 109, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 21, 22, 25, 28, 29, 36] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003826 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003826 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003826/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003826 Building REAL300000003827 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003827' /scratch/stefan/7769584/working/building/REAL300000003827 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003827 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003827/0 /scratch/stefan/7769584/working/building/REAL300000003827 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/941 `/scratch/stefan/7769584/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)C([N+](=O)[O-])=C1) `REAL300000003827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003827 none NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 11, 37, 37, 11, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 17, 17, 17, 17, 17, 37, 37, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 17] 43 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 19, 20, 22, 23, 24, 25, 26, 27, 28, 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: REAL300000003827 none NS(=O)(=O)C1=CC=C(N=NC2CCC3=CC=CC(C(=O)[O-])=C32)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 17, 1, 1, 2, 2, 1, 5, 5, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 1] 43 rigid atoms, others: [1, 4, 5, 6, 7, 8, 39, 22, 23, 26, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003827 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003827 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003827/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003827 Building REAL300000003828 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003828' /scratch/stefan/7769584/working/building/REAL300000003828 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003828 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003828/0 /scratch/stefan/7769584/working/building/REAL300000003828 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/942 `/scratch/stefan/7769584/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CN=CC(C(=O)[O-])=C1) `REAL300000003828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003828 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 72, 72, 119, 119, 72, 99, 201, 201, 201, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 119, 119, 201, 201, 119, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 17, 18, 19, 20, 21, 22, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 860 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003828 none CC(N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-])C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 1, 1, 1, 2, 2, 33, 119, 119, 119, 119, 119, 119, 119, 119, 33, 33, 33, 33, 1, 1, 5, 5, 1, 119, 119, 119] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 12, 13, 14, 30, 31] set([0, 1, 2, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 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/7769584/working/building/REAL300000003828 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003828 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003828/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003828 Building REAL300000003829 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003829' /scratch/stefan/7769584/working/building/REAL300000003829 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003829 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003829/0 /scratch/stefan/7769584/working/building/REAL300000003829 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/943 `/scratch/stefan/7769584/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N=C2)C([N+](=O)[O-])=C1) `REAL300000003829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003829 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 100, 201, 201, 100, 100, 100, 61, 61, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 201, 201, 100, 100, 9, 9, 1, 1, 1, 100] 201 rigid atoms, others: [32, 33, 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, 34]) total number of confs: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003829 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])N=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 4, 4, 1, 1, 1, 1, 1, 3, 3, 19, 100, 100, 99, 99, 100, 100, 100, 100, 1, 1, 2, 2, 1, 5, 5, 1, 1, 19, 19, 100, 100, 100, 1] 201 rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 20, 21, 24, 27, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003829 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003829 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003829/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003829 Building REAL300000003830 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003830' /scratch/stefan/7769584/working/building/REAL300000003830 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003830 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003830/0 /scratch/stefan/7769584/working/building/REAL300000003830 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/944 `/scratch/stefan/7769584/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)C([N+](=O)[O-])=C1) `REAL300000003830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003830 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [195, 64, 195, 195, 64, 73, 73, 64, 64, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 73, 73, 74, 74, 73, 196, 196, 73, 73, 8, 8, 1, 1, 2, 1, 73] 402 rigid atoms, others: [32, 33, 35, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 36]) total number of confs: 705 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003830 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(C(=O)[O-])C(O)=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 16, 73, 73, 73, 73, 103, 103, 73, 73, 73, 1, 1, 2, 2, 1, 5, 5, 1, 1, 16, 16, 73, 73, 146, 73, 1] 402 rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003830 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003830 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003830/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003830 Building REAL300000003831 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003831' /scratch/stefan/7769584/working/building/REAL300000003831 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003831 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003831/0 /scratch/stefan/7769584/working/building/REAL300000003831 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/945 `/scratch/stefan/7769584/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])C=C1C(=O)[O-]) `REAL300000003831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003831 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [63, 63, 63, 63, 14, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 63, 63, 63, 102, 102, 63, 63, 63, 63, 63, 13, 14, 1, 1, 5, 5, 1, 63] 201 rigid atoms, others: [33, 34, 37, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003831 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 58, 59, 63, 63, 59, 59, 199, 199, 199, 63, 63, 63, 63, 63, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 8, 63, 63, 199, 199, 63, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003831 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003831 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003831/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003831 Building REAL300000003832 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003832' /scratch/stefan/7769584/working/building/REAL300000003832 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003832 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003832/0 /scratch/stefan/7769584/working/building/REAL300000003832 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/946 `/scratch/stefan/7769584/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003832 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [36, 36, 36, 24, 30, 36, 36, 36, 36, 22, 6, 22, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 36, 36, 36, 36, 36, 36, 22, 22, 22, 22, 1, 1, 5, 5, 1] 81 rigid atoms, others: [37, 38, 41, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) 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: REAL300000003832 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 36, 36, 26, 26, 72, 72, 72, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 36, 36, 72, 72, 36] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003832 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003832 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003832/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003832 Building REAL300000003833 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003833' /scratch/stefan/7769584/working/building/REAL300000003833 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003833 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003833/0 /scratch/stefan/7769584/working/building/REAL300000003833 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/947 `/scratch/stefan/7769584/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC(Cl)=NC=C2C(=O)[O-])C([N+](=O)[O-])=C1) `REAL300000003833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003833 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(Cl)=NC=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 53, 169, 169, 53, 100, 100, 53, 53, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 100, 100, 100, 100, 100, 169, 169, 100, 100, 8, 8, 1, 1, 100] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003833 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(Cl)=NC=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 42, 100, 100, 100, 42, 100, 100, 100, 106, 106, 1, 1, 2, 2, 1, 5, 5, 1, 1, 42, 42, 100, 100, 1] 201 rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003833 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003833/1 /scratch/stefan/7769584/working/building/REAL300000003833 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/948 `/scratch/stefan/7769584/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C([N+](=O)[O-])=C1) `REAL300000003833.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003833 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 3, 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, 34, 119, 119, 34, 46, 46, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 46, 46, 46, 46, 46, 119, 119, 46, 46, 34, 6, 1, 1, 46] 119 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003833 none NS(=O)(=O)C1=CC=C(NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 28, 28, 46, 46, 46, 46, 46, 46, 46, 49, 49, 1, 1, 2, 2, 1, 5, 5, 1, 1, 6, 28, 46, 46, 1] 119 rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 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/7769584/working/building/REAL300000003833 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003833 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003833/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003833/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003833 Building REAL300000003834 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003834' /scratch/stefan/7769584/working/building/REAL300000003834 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003834 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003834/0 /scratch/stefan/7769584/working/building/REAL300000003834 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/949 `/scratch/stefan/7769584/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003834 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [89, 89, 89, 89, 89, 89, 89, 89, 23, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 89, 89, 89, 89, 23, 22, 1, 1, 5, 5, 1] 201 rigid atoms, others: [32, 35, 11, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 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: REAL300000003834 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 89, 89, 50, 50, 159, 159, 159, 89, 89, 89, 89, 89, 2, 2, 2, 1, 8, 8, 89, 89, 159, 159, 89] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003834 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003834 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003834/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003834 Building REAL300000003835 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003835' /scratch/stefan/7769584/working/building/REAL300000003835 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003835 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003835/0 /scratch/stefan/7769584/working/building/REAL300000003835 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/950 `/scratch/stefan/7769584/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003835 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 24, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 90, 90, 90, 90, 90, 23, 24, 1, 1, 5, 5, 1] 201 rigid atoms, others: [32, 33, 36, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003835 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 52, 52, 90, 90, 52, 52, 163, 163, 163, 90, 90, 90, 90, 90, 2, 2, 2, 1, 1, 8, 8, 90, 90, 163, 163, 90] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 28, 29] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003835 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003835 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003835/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003835 Building REAL300000003836 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003836' /scratch/stefan/7769584/working/building/REAL300000003836 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003836 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003836/0 /scratch/stefan/7769584/working/building/REAL300000003836 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/951 `/scratch/stefan/7769584/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])O1) `REAL300000003836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003836 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 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: [71, 71, 71, 71, 94, 94, 71, 15, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 71, 71, 71, 71, 71, 14, 15, 1, 1, 5, 5, 1] 201 rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) 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: REAL300000003836 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 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: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 59, 59, 71, 71, 59, 59, 201, 201, 201, 71, 71, 71, 71, 71, 1, 2, 2, 2, 1, 8, 8, 71, 71, 201, 201, 71] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003836 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003836 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003836/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003836 Building REAL300000003837 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003837' /scratch/stefan/7769584/working/building/REAL300000003837 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003837 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003837/0 /scratch/stefan/7769584/working/building/REAL300000003837 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/952 `/scratch/stefan/7769584/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)[O-])=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])S1) `REAL300000003837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003837 none CCC1=CC(C(=O)[O-])=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [55, 37, 37, 37, 37, 37, 41, 41, 22, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 37, 55, 55, 55, 55, 55, 37, 21, 22, 1, 1, 5, 5, 1] 149 rigid atoms, others: [34, 35, 38, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) 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: REAL300000003837 none CCC1=CC(C(=O)[O-])=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 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: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 24, 24, 37, 37, 24, 24, 97, 97, 97, 37, 37, 37, 37, 37, 1, 8, 8, 8, 8, 8, 1, 5, 5, 37, 37, 97, 97, 37] 149 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 25, 31] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003837 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003837 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003837/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003837 Building REAL300000003838 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003838' /scratch/stefan/7769584/working/building/REAL300000003838 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003838 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003838/0 /scratch/stefan/7769584/working/building/REAL300000003838 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/953 `/scratch/stefan/7769584/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003838 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)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', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [97, 75, 75, 75, 75, 75, 75, 75, 75, 75, 28, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 97, 97, 97, 75, 75, 75, 27, 28, 1, 1, 5, 5, 1] 201 rigid atoms, others: [35, 36, 39, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) 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: REAL300000003838 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=C(S(N)(=O)=O)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', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 51, 52, 75, 75, 52, 52, 193, 193, 193, 75, 75, 75, 75, 75, 4, 4, 4, 1, 1, 1, 8, 8, 75, 75, 193, 193, 75] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003838 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003838 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003838/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003838 Building REAL300000003839 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003839' /scratch/stefan/7769584/working/building/REAL300000003839 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003839 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003839/0 /scratch/stefan/7769584/working/building/REAL300000003839 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/954 `/scratch/stefan/7769584/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)C([N+](=O)[O-])=C1) `REAL300000003839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003839 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 117, 201, 201, 99, 117, 117, 62, 61, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 117, 117, 117, 117, 117, 201, 201, 117, 117, 8, 8, 1, 1, 117] 201 rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003839 none NS(=O)(=O)C1=CC=C(N=NCC2=CC(C(=O)[O-])=CO2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 29, 116, 116, 116, 117, 117, 116, 116, 1, 1, 2, 2, 1, 5, 5, 1, 1, 29, 29, 116, 116, 1] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 19, 20, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 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/7769584/working/building/REAL300000003839 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003839 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003839/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003839 Building REAL300000003840 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003840' /scratch/stefan/7769584/working/building/REAL300000003840 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003840 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003840/0 /scratch/stefan/7769584/working/building/REAL300000003840 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/955 `/scratch/stefan/7769584/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])C(C(=O)[O-])=C1) `REAL300000003840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003840 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 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: [98, 98, 98, 98, 42, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 98, 98, 100, 100, 98, 98, 98, 98, 98, 98, 41, 42, 1, 1, 5, 5, 1, 98] 201 rigid atoms, others: [33, 34, 37, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003840 none CC1=CC=C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 50, 51, 98, 98, 51, 51, 171, 171, 171, 98, 98, 98, 98, 98, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 8, 8, 98, 98, 171, 171, 98, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003840 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003840 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003840/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003840 Building REAL300000003841 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003841' /scratch/stefan/7769584/working/building/REAL300000003841 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003841 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003841/0 /scratch/stefan/7769584/working/building/REAL300000003841 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/956 `/scratch/stefan/7769584/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=CC=C1C(=O)[O-]) `REAL300000003841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003841 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 49, 49, 49, 10, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 49, 49, 49, 49, 81, 81, 83, 83, 83, 49, 9, 10, 1, 1, 5, 5, 1, 49, 49] 201 rigid atoms, others: [33, 34, 37, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39]) 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: REAL300000003841 none COC1=CC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 46, 46, 49, 49, 46, 46, 133, 133, 133, 49, 49, 49, 49, 49, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 9, 49, 49, 133, 133, 49, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 21, 22, 23, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003841 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003841 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003841/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003841 Building REAL300000003842 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003842' /scratch/stefan/7769584/working/building/REAL300000003842 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003842 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003842/0 /scratch/stefan/7769584/working/building/REAL300000003842 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/957 `/scratch/stefan/7769584/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1) `REAL300000003842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003842 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [79, 79, 79, 79, 111, 111, 79, 19, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 79, 79, 79, 79, 79, 18, 19, 1, 1, 5, 5, 1, 79] 201 rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36]) 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: REAL300000003842 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 63, 63, 79, 79, 63, 63, 193, 193, 193, 79, 79, 79, 79, 79, 1, 2, 2, 2, 1, 9, 9, 79, 79, 193, 193, 79, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 24, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003842 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003842 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003842/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003842 Building REAL300000003843 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003843' /scratch/stefan/7769584/working/building/REAL300000003843 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003843 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003843/0 /scratch/stefan/7769584/working/building/REAL300000003843 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/958 `/scratch/stefan/7769584/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=C(C(=O)[O-])C=CS2)C([N+](=O)[O-])=C1) `REAL300000003843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003843 none NS(=O)(=O)C1=CC=C(N=NCC2=C(C(=O)[O-])C=CS2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 48, 178, 178, 48, 68, 68, 48, 47, 8, 1, 1, 1, 1, 3, 3, 1, 1, 1, 68, 68, 68, 68, 68, 178, 178, 68, 68, 8, 8, 1, 1, 68] 201 rigid atoms, others: [10, 11, 12, 13, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 687 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003843 none NS(=O)(=O)C1=CC=C(N=NCC2=C(C(=O)[O-])C=CS2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 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] 0 hydrogens 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, 5, 5, 29, 67, 68, 103, 103, 67, 67, 67, 1, 1, 2, 2, 1, 5, 5, 1, 1, 29, 29, 67, 67, 1] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 19, 20, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 28, 29, 30, 31]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003843 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003843 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003843/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003843 Building REAL300000003844 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003844' /scratch/stefan/7769584/working/building/REAL300000003844 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003844 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003844/0 /scratch/stefan/7769584/working/building/REAL300000003844 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/959 `/scratch/stefan/7769584/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1) `REAL300000003844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003844 none NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 16, 51, 51, 16, 19, 19, 16, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 19, 19, 19, 19, 51, 51, 19, 19, 16, 6, 1, 1, 19] 51 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) 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: REAL300000003844 none NS(=O)(=O)C1=CC=C(NN=CC2=CSC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 6, 16, 16, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 5, 5, 1, 1, 6, 16, 19, 19, 1] 51 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 19, 20, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003844 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003844/1 /scratch/stefan/7769584/working/building/REAL300000003844 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/960 `/scratch/stefan/7769584/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CSC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1) `REAL300000003844.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003844 none NS(=O)(=O)C1=CC=C(N=NCC2=CSC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 14, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 101, 201, 201, 65, 119, 119, 65, 65, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 119, 119, 119, 119, 119, 201, 201, 119, 119, 9, 9, 1, 1, 119] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003844 none NS(=O)(=O)C1=CC=C(N=NCC2=CSC(C(=O)[O-])=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 14, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 33, 119, 119, 119, 119, 119, 119, 119, 1, 1, 2, 2, 1, 5, 5, 1, 1, 33, 33, 119, 119, 1] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 19, 20, 23, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 28, 29, 30, 31]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003844 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003844 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003844/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003844/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003844 Building REAL300000003845 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003845' /scratch/stefan/7769584/working/building/REAL300000003845 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003845 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003845/0 /scratch/stefan/7769584/working/building/REAL300000003845 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/961 `/scratch/stefan/7769584/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)C([N+](=O)[O-])=C1) `REAL300000003845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003845 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [128, 48, 128, 128, 48, 54, 54, 48, 48, 8, 1, 1, 1, 1, 1, 1, 6, 14, 25, 23, 1, 54, 54, 54, 54, 54, 128, 128, 54, 54, 8, 8, 1, 1, 6, 6, 14, 14, 54] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) 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: REAL300000003845 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=C(CCC(=O)[O-])O2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', '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: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 3, 3, 17, 54, 54, 54, 54, 93, 104, 114, 114, 54, 1, 1, 2, 2, 1, 5, 5, 1, 1, 17, 17, 54, 54, 93, 93, 104, 104, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 22, 25, 38, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003845 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003845 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003845/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003845 Building REAL300000003846 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003846' /scratch/stefan/7769584/working/building/REAL300000003846 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003846 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003846/0 /scratch/stefan/7769584/working/building/REAL300000003846 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/962 `/scratch/stefan/7769584/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(F)=C2C(=O)[O-])C([N+](=O)[O-])=C1) `REAL300000003846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003846 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(F)=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [178, 53, 178, 178, 53, 101, 101, 53, 53, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 101, 101, 101, 101, 101, 178, 178, 101, 101, 8, 8, 1, 1, 1, 101] 199 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 809 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003846 none NS(=O)(=O)C1=CC=C(N=NCC2=CC=CC(F)=C2C(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 42, 101, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 2, 2, 1, 5, 5, 1, 1, 42, 42, 101, 101, 101, 1] 199 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003846 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003846 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003846/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003846 Building REAL300000003847 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003847' /scratch/stefan/7769584/working/building/REAL300000003847 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003847 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003847/0 /scratch/stefan/7769584/working/building/REAL300000003847 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/963 `/scratch/stefan/7769584/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)[O-])C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1) `REAL300000003847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003847 none N#CC1=CC=C(C(=O)[O-])C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [86, 86, 86, 86, 86, 86, 86, 86, 86, 38, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 86, 86, 86, 37, 38, 1, 1, 5, 5, 1, 86] 201 rigid atoms, others: [32, 35, 12, 13, 14, 15, 16, 17, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003847 none N#CC1=CC=C(C(=O)[O-])C(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 53, 53, 86, 86, 53, 53, 179, 179, 179, 86, 86, 86, 86, 86, 1, 1, 1, 8, 8, 86, 86, 179, 179, 86, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 36, 26, 27, 28] set([7, 8, 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: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003847 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003847 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003847/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003847 Building REAL300000003848 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003848' /scratch/stefan/7769584/working/building/REAL300000003848 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003848 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003848/0 /scratch/stefan/7769584/working/building/REAL300000003848 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/964 `/scratch/stefan/7769584/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1C(=O)[O-]) `REAL300000003848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003848 none CC1=NSC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 28, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 82, 82, 110, 110, 82, 82, 82, 27, 28, 1, 1, 5, 5, 1] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: REAL300000003848 none CC1=NSC(CN=NC2=CC=C(S(N)(=O)=O)C=C2[N+](=O)[O-])=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 53, 53, 82, 82, 53, 53, 183, 183, 183, 82, 82, 82, 82, 82, 1, 1, 3, 3, 2, 2, 2, 8, 8, 82, 82, 183, 183, 82] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003848 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003848 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003848/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003848 Building REAL300000003849 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003849' /scratch/stefan/7769584/working/building/REAL300000003849 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003849 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003849/0 /scratch/stefan/7769584/working/building/REAL300000003849 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/965 `/scratch/stefan/7769584/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-]) `REAL300000003849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003849 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [97, 67, 67, 67, 67, 67, 67, 67, 67, 67, 21, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 97, 97, 97, 67, 67, 67, 20, 21, 1, 1, 5, 5, 1] 201 rigid atoms, others: [35, 36, 39, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300000003849 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=C(S(N)(=O)=O)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 53, 54, 67, 67, 54, 54, 201, 201, 201, 67, 67, 67, 67, 67, 4, 4, 4, 1, 1, 1, 8, 8, 67, 67, 201, 201, 67] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003849 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003849 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003849/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003849 Building REAL300000003850 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003850' /scratch/stefan/7769584/working/building/REAL300000003850 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003850 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003850/0 /scratch/stefan/7769584/working/building/REAL300000003850 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/966 `/scratch/stefan/7769584/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)C=C1) `REAL300000003850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003850 none O=C([O-])C1=CC=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 119, 190, 55, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 108, 108, 68, 68, 31, 31, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 823 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003850 none O=C([O-])C1=CC=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 25, 47, 134, 201, 201, 176, 201, 201, 201, 201, 1, 1, 1, 1, 5, 8, 23, 23, 31, 31, 42, 42, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/7769584/working/building/REAL300000003850 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003850 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003850/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003850 Building REAL300000003851 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003851' /scratch/stefan/7769584/working/building/REAL300000003851 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003851 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003851/0 /scratch/stefan/7769584/working/building/REAL300000003851 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/967 `/scratch/stefan/7769584/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl) `REAL300000003851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003851 none O=C([O-])C1=CC=CC=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 175, 175, 71, 175, 51, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 195, 175, 69, 69, 55, 55, 28, 28, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003851 none O=C([O-])C1=CC=CC=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 32, 32, 59, 155, 201, 201, 193, 201, 201, 201, 201, 1, 1, 1, 1, 4, 8, 32, 32, 40, 40, 53, 53, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 527 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003851 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003851 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003851/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003851 Building REAL300000003852 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003852' /scratch/stefan/7769584/working/building/REAL300000003852 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003852 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003852/0 /scratch/stefan/7769584/working/building/REAL300000003852 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/968 `/scratch/stefan/7769584/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)N1) `REAL300000003852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003852 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 201, 201, 201, 201, 194, 194, 90, 194, 50, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 194, 82, 82, 62, 62, 28, 28, 1, 1, 1, 201] 201 rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003852 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 4, 4, 4, 13, 17, 32, 111, 201, 201, 149, 201, 201, 201, 201, 1, 2, 2, 2, 1, 2, 4, 13, 13, 21, 21, 28, 28, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 41, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003852 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003852 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003852/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003852 Building REAL300000003853 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003853' /scratch/stefan/7769584/working/building/REAL300000003853 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003853 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003853/0 /scratch/stefan/7769584/working/building/REAL300000003853 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/969 `/scratch/stefan/7769584/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=CC=C1) `REAL300000003853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003853 none O=C([O-])C1=CC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 193, 193, 189, 189, 90, 189, 50, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 193, 189, 82, 82, 62, 62, 28, 28, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003853 none O=C([O-])C1=CC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 23, 27, 44, 141, 201, 201, 177, 201, 201, 201, 201, 1, 1, 1, 1, 3, 5, 23, 23, 31, 31, 40, 40, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 23, 24, 25, 26, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003853 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003853 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003853/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003853 Building REAL300000003854 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003854' /scratch/stefan/7769584/working/building/REAL300000003854 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003854 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003854/0 /scratch/stefan/7769584/working/building/REAL300000003854 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/970 `/scratch/stefan/7769584/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=CN1) `REAL300000003854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003854 none O=C([O-])C1=CC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations 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, 196, 196, 194, 194, 106, 194, 54, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 194, 95, 96, 68, 68, 30, 30, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 788 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003854 none O=C([O-])C1=CC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 24, 26, 49, 143, 201, 201, 185, 201, 201, 201, 201, 1, 1, 1, 5, 7, 24, 24, 32, 32, 44, 44, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 38, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003854 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003854 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003854/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003854 Building REAL300000003855 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003855' /scratch/stefan/7769584/working/building/REAL300000003855 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003855 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003855/0 /scratch/stefan/7769584/working/building/REAL300000003855 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/971 `/scratch/stefan/7769584/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)C=N1) `REAL300000003855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003855 none O=C([O-])C1=CC=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 123, 123, 123, 123, 85, 123, 50, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 123, 123, 79, 79, 60, 60, 26, 26, 1, 1, 1, 201] 201 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) 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: REAL300000003855 none O=C([O-])C1=CC=C(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 19, 25, 47, 132, 201, 201, 164, 201, 201, 201, 201, 1, 1, 1, 1, 2, 4, 19, 19, 33, 33, 41, 41, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003855 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003855 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003855/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003855 Building REAL300000003856 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003856' /scratch/stefan/7769584/working/building/REAL300000003856 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003856 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003856/0 /scratch/stefan/7769584/working/building/REAL300000003856 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/972 `/scratch/stefan/7769584/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl) `REAL300000003856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003856 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 193, 193, 100, 193, 48, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 194, 193, 89, 90, 61, 61, 29, 29, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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]) total number of confs: 765 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003856 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 21, 25, 46, 140, 201, 201, 180, 201, 201, 201, 201, 2, 2, 2, 1, 4, 5, 21, 21, 29, 29, 42, 42, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003856 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003856 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003856/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003856 Building REAL300000003857 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003857' /scratch/stefan/7769584/working/building/REAL300000003857 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003857 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003857/0 /scratch/stefan/7769584/working/building/REAL300000003857 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/973 `/scratch/stefan/7769584/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl) `REAL300000003857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003857 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 191, 191, 95, 191, 48, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 86, 86, 60, 60, 28, 28, 1, 1, 1] 201 rigid atoms, others: [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, 38]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003857 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)CCCOC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 24, 43, 141, 201, 201, 180, 201, 201, 201, 201, 2, 2, 2, 1, 1, 4, 4, 20, 20, 28, 28, 39, 39, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 29, 30] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003857 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003857 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003857/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003857 Building REAL300000003858 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003858' /scratch/stefan/7769584/working/building/REAL300000003858 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003858 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003858/0 /scratch/stefan/7769584/working/building/REAL300000003858 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/974 `/scratch/stefan/7769584/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=C1) `REAL300000003858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003858 none O=C([O-])C1=COC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 149, 149, 141, 141, 77, 141, 46, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 149, 141, 73, 73, 56, 56, 24, 24, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 707 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003858 none O=C([O-])C1=COC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 31, 35, 57, 144, 201, 201, 199, 201, 201, 201, 201, 1, 1, 7, 16, 31, 31, 43, 43, 50, 50, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003858 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003858 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003858/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003858 Building REAL300000003859 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003859' /scratch/stefan/7769584/working/building/REAL300000003859 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003859 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003859/0 /scratch/stefan/7769584/working/building/REAL300000003859 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/975 `/scratch/stefan/7769584/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=C1) `REAL300000003859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003859 none CC1=C(C(=O)[O-])NC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 128, 128, 122, 122, 67, 122, 42, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 128, 122, 63, 63, 48, 48, 24, 24, 1, 1, 1, 201] 201 rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) 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: REAL300000003859 none CC1=C(C(=O)[O-])NC(C=NNC(=O)CCCOC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 3, 3, 7, 7, 7, 21, 25, 49, 118, 201, 201, 146, 174, 201, 201, 201, 1, 2, 2, 2, 1, 3, 7, 21, 21, 33, 33, 41, 41, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 41, 25, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003859 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003859 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003859/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003859 Building REAL300000003860 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003860' /scratch/stefan/7769584/working/building/REAL300000003860 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003860 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003860/0 /scratch/stefan/7769584/working/building/REAL300000003860 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/976 `/scratch/stefan/7769584/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1) `REAL300000003860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003860 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 189, 201, 201, 189, 189, 150, 150, 52, 150, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 189, 150, 52, 52, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 578 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: REAL300000003860 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 56, 171, 201, 201, 192, 201, 201, 201, 201, 1, 1, 1, 1, 6, 14, 56, 56, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 447 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003860 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003860 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003860/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003860 Building REAL300000003861 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003861' /scratch/stefan/7769584/working/building/REAL300000003861 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003861 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003861/0 /scratch/stefan/7769584/working/building/REAL300000003861 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/977 `/scratch/stefan/7769584/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003861 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 171, 87, 87, 87, 81, 87, 87, 81, 81, 81, 81, 31, 81, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 87, 87, 87, 87, 81, 81, 31, 31, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003861 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 14, 39, 87, 87, 59, 63, 87, 87, 87, 19, 19, 1, 1, 1, 1, 4, 4, 14, 14, 87, 87, 87] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 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: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003861 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003861 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003861/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003861 Building REAL300000003862 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003862' /scratch/stefan/7769584/working/building/REAL300000003862 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003862 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003862/0 /scratch/stefan/7769584/working/building/REAL300000003862 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/978 `/scratch/stefan/7769584/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1) `REAL300000003862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003862 none O=C([O-])COC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 176, 111, 111, 111, 111, 69, 69, 69, 69, 33, 69, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 201, 201, 111, 111, 69, 69, 33, 33, 1, 1, 1, 111, 111] 201 rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 580 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003862 none O=C([O-])COC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 11, 53, 111, 111, 79, 111, 111, 111, 111, 1, 1, 9, 9, 1, 1, 2, 2, 11, 11, 111, 111, 111, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 25, 38, 28, 29, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003862 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003862 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003862/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003862 Building REAL300000003863 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003863' /scratch/stefan/7769584/working/building/REAL300000003863 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003863 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003863/0 /scratch/stefan/7769584/working/building/REAL300000003863 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/979 `/scratch/stefan/7769584/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003863 none O=C([O-])C1=CC=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 160, 160, 41, 160, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 166, 160, 41, 41, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 505 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: REAL300000003863 none O=C([O-])C1=CC=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 1, 1, 1, 4, 4, 8, 8, 8, 31, 132, 201, 201, 182, 199, 201, 201, 201, 1, 1, 1, 1, 4, 8, 31, 31, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 448 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003863 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003863 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003863/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003863 Building REAL300000003864 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003864' /scratch/stefan/7769584/working/building/REAL300000003864 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003864 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003864/0 /scratch/stefan/7769584/working/building/REAL300000003864 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/980 `/scratch/stefan/7769584/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1) `REAL300000003864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003864 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 14, 14, 14, 53, 163, 201, 201, 197, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 53, 53, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 414 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: REAL300000003864 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 114, 114, 43, 114, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 118, 118, 201, 201, 201, 201, 118, 118, 118, 114, 43, 43, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 997 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003864 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003864 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003864/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003864 Building REAL300000003865 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003865' /scratch/stefan/7769584/working/building/REAL300000003865 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003865 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003865/0 /scratch/stefan/7769584/working/building/REAL300000003865 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/981 `/scratch/stefan/7769584/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000003865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003865 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 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, 6, 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] 0 hydrogens 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, 10, 10, 10, 41, 120, 169, 169, 156, 169, 169, 169, 169, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 10, 41, 41, 169, 169, 169, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [1, 35, 36, 39, 40, 16, 17, 18, 19, 20, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 410 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003865 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 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, 6, 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] 0 hydrogens 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, 98, 94, 94, 37, 94, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 169, 169, 103, 98, 201, 201, 201, 169, 169, 98, 98, 98, 94, 37, 37, 1, 1, 1, 169, 169, 201, 201, 169, 169] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 1095 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003865 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003865 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003865/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003865 Building REAL300000003866 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003866' /scratch/stefan/7769584/working/building/REAL300000003866 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003866 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003866/0 /scratch/stefan/7769584/working/building/REAL300000003866 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/982 `/scratch/stefan/7769584/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1) `REAL300000003866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003866 none O=C([O-])COC1=CC=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 70, 70, 70, 70, 70, 68, 68, 68, 68, 31, 68, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 70, 70, 70, 68, 68, 31, 31, 1, 1, 1, 70] 201 rigid atoms, others: [35, 36, 37, 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, 38]) 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: REAL300000003866 none O=C([O-])COC1=CC=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 19, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 11, 36, 70, 70, 51, 68, 70, 70, 70, 1, 11, 11, 1, 1, 1, 3, 3, 11, 11, 70, 70, 70, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 25, 38, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003866 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003866 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003866/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003866 Building REAL300000003867 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003867' /scratch/stefan/7769584/working/building/REAL300000003867 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003867 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003867/0 /scratch/stefan/7769584/working/building/REAL300000003867 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/983 `/scratch/stefan/7769584/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N1) `REAL300000003867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003867 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 142, 142, 113, 113, 40, 113, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 113, 40, 40, 1, 1, 1, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000003867 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 57, 157, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 7, 17, 57, 57, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003867 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003867 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003867/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003867 Building REAL300000003868 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003868' /scratch/stefan/7769584/working/building/REAL300000003868 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003868 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003868/0 /scratch/stefan/7769584/working/building/REAL300000003868 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/984 `/scratch/stefan/7769584/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1) `REAL300000003868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003868 none CCC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 1, 7, 7, 17, 17, 17, 65, 139, 174, 174, 161, 170, 174, 174, 174, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 12, 12, 17, 65, 65, 174, 174, 174, 1, 1, 1, 1] 201 rigid atoms, others: [2, 37, 38, 39, 40, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 491 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: REAL300000003868 none CCC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 119, 119, 95, 95, 38, 95, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 174, 174, 119, 164, 174, 174, 174, 174, 156, 156, 156, 156, 156, 95, 38, 38, 1, 1, 1, 174, 174, 174, 174] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 911 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003868 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003868 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003868/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003868 Building REAL300000003869 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003869' /scratch/stefan/7769584/working/building/REAL300000003869 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003869 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003869/0 /scratch/stefan/7769584/working/building/REAL300000003869 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/985 `/scratch/stefan/7769584/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=CC=C1C(=O)[O-]) `REAL300000003869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003869 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 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, 3, 5, 5, 5, 45, 156, 201, 201, 189, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 5, 45, 45, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 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]) total number of confs: 442 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003869 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 135, 135, 38, 135, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 135, 38, 38, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 503 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003869 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003869 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003869/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003869 Building REAL300000003870 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003870' /scratch/stefan/7769584/working/building/REAL300000003870 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003870 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003870/0 /scratch/stefan/7769584/working/building/REAL300000003870 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/986 `/scratch/stefan/7769584/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000003870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003870 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 17, 17, 17, 57, 157, 201, 201, 199, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 17, 57, 57, 201, 201, 201, 1, 1, 1, 2] 402 rigid atoms, others: [1, 35, 36, 37, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 434 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: REAL300000003870 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [100, 100, 91, 91, 39, 91, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 91, 39, 39, 1, 1, 1, 201, 201, 201, 402] 402 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 851 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003870 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003870 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003870/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003870 Building REAL300000003871 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003871' /scratch/stefan/7769584/working/building/REAL300000003871 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003871 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003871/0 /scratch/stefan/7769584/working/building/REAL300000003871 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/987 `/scratch/stefan/7769584/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=CC(C(=O)[O-])=C1) `REAL300000003871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003871 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 10, 10, 45, 145, 201, 201, 192, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 2, 1, 6, 6, 6, 10, 45, 45, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 444 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: REAL300000003871 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 132, 132, 41, 132, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 132, 41, 41, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 510 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003871 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003871 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003871/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003871 Building REAL300000003872 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003872' /scratch/stefan/7769584/working/building/REAL300000003872 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003872 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003872/0 /scratch/stefan/7769584/working/building/REAL300000003872 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/988 `/scratch/stefan/7769584/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N=N1) `REAL300000003872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003872 none O=C([O-])CN1C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 155, 155, 155, 79, 79, 79, 79, 31, 79, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 155, 79, 79, 31, 31, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000003872 none O=C([O-])CN1C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 25, 85, 155, 155, 113, 122, 155, 155, 155, 1, 1, 6, 6, 1, 7, 7, 25, 25, 155, 155, 155] 201 rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 26] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003872 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003872 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003872/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003872 Building REAL300000003873 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003873' /scratch/stefan/7769584/working/building/REAL300000003873 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003873 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003873/0 /scratch/stefan/7769584/working/building/REAL300000003873 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/989 `/scratch/stefan/7769584/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000003873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003873 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 11, 11, 11, 41, 118, 201, 201, 161, 191, 201, 201, 201, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 11, 41, 41, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 569 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003873 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 36, 66, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 66, 36, 36, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 408 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003873 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003873 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003873/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003873 Building REAL300000003874 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003874' /scratch/stefan/7769584/working/building/REAL300000003874 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003874 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003874/0 /scratch/stefan/7769584/working/building/REAL300000003874 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/990 `/scratch/stefan/7769584/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1) `REAL300000003874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003874 none O=C([O-])C1=CSC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 162, 162, 125, 125, 42, 125, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 162, 125, 42, 42, 1, 1, 1, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 502 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: REAL300000003874 none O=C([O-])C1=CSC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 58, 163, 201, 201, 201, 201, 201, 201, 201, 1, 1, 7, 15, 58, 58, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 426 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003874 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003874 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003874/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003874 Building REAL300000003875 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003875' /scratch/stefan/7769584/working/building/REAL300000003875 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003875 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003875/0 /scratch/stefan/7769584/working/building/REAL300000003875 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/991 `/scratch/stefan/7769584/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CC=C1O) `REAL300000003875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003875 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 192, 169, 169, 45, 169, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 169, 45, 45, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 919 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: REAL300000003875 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 33, 124, 201, 201, 170, 183, 201, 201, 201, 1, 1, 1, 1, 1, 3, 5, 33, 33, 201, 201, 201, 1, 1, 2] 402 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, 35]) total number of confs: 473 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003875 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003875 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003875/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003875 Building REAL300000003876 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003876' /scratch/stefan/7769584/working/building/REAL300000003876 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003876 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003876/0 /scratch/stefan/7769584/working/building/REAL300000003876 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/992 `/scratch/stefan/7769584/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000003876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003876 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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: [7, 1, 7, 7, 11, 11, 11, 52, 157, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 52, 52, 201, 201, 201, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 421 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003876 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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: [150, 150, 128, 128, 41, 128, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 128, 41, 41, 1, 1, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 502 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003876 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003876 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003876/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003876 Building REAL300000003877 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003877' /scratch/stefan/7769584/working/building/REAL300000003877 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003877 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003877/0 /scratch/stefan/7769584/working/building/REAL300000003877 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/993 `/scratch/stefan/7769584/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])O1) `REAL300000003877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003877 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 58, 155, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 58, 58, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 33, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 410 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: REAL300000003877 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 166, 166, 53, 166, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 166, 53, 53, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 535 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003877 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003877 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003877/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003877 Building REAL300000003878 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003878' /scratch/stefan/7769584/working/building/REAL300000003878 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003878 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003878/0 /scratch/stefan/7769584/working/building/REAL300000003878 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/994 `/scratch/stefan/7769584/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N1) `REAL300000003878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003878 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 48, 179, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 179, 48, 48, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 529 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: REAL300000003878 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 33, 113, 201, 201, 156, 194, 201, 201, 201, 1, 2, 2, 2, 1, 4, 8, 33, 33, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 35, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 552 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003878 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003878 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003878/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003878 Building REAL300000003879 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003879' /scratch/stefan/7769584/working/building/REAL300000003879 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003879 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003879/0 /scratch/stefan/7769584/working/building/REAL300000003879 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/995 `/scratch/stefan/7769584/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C1) `REAL300000003879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003879 none O=C([O-])C1CC(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 174, 174, 40, 174, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 174, 40, 40, 1, 1, 1, 201, 201] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 510 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003879 none O=C([O-])C1CC(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 24, 107, 201, 201, 163, 201, 201, 201, 201, 1, 1, 1, 1, 3, 24, 24, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003879 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003879 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003879/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003879 Building REAL300000003880 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003880' /scratch/stefan/7769584/working/building/REAL300000003880 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003880 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003880/0 /scratch/stefan/7769584/working/building/REAL300000003880 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/996 `/scratch/stefan/7769584/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CC=C1) `REAL300000003880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003880 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 200, 200, 170, 170, 48, 170, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 170, 48, 48, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 513 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: REAL300000003880 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 6, 7, 7, 47, 144, 201, 201, 191, 201, 201, 201, 201, 1, 1, 1, 1, 3, 6, 47, 47, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 445 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003880 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003880 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003880/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003880 Building REAL300000003881 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003881' /scratch/stefan/7769584/working/building/REAL300000003881 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003881 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003881/0 /scratch/stefan/7769584/working/building/REAL300000003881 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/997 `/scratch/stefan/7769584/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CSC(C(=O)[O-])=C1) `REAL300000003881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003881 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 8, 14, 14, 14, 47, 159, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 1, 8, 8, 8, 14, 47, 47, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 33, 16, 17, 18, 19, 20, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 391 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: REAL300000003881 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 135, 129, 129, 43, 129, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 129, 43, 43, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 516 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003881 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003881 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003881/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003881 Building REAL300000003882 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003882' /scratch/stefan/7769584/working/building/REAL300000003882 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003882 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003882/0 /scratch/stefan/7769584/working/building/REAL300000003882 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/998 `/scratch/stefan/7769584/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003882 none CC(CCCCCCC(=O)[O-])=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 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, 2, 2, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 109, 100, 151, 140, 159, 201, 201, 201, 20, 20, 14, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 109, 109, 127, 127, 141, 142, 160, 160, 162, 162, 199, 200, 20, 14, 14, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 1187 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003882 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003882 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003882/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003882 Building REAL300000003883 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003883' /scratch/stefan/7769584/working/building/REAL300000003883 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003883 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003883/0 /scratch/stefan/7769584/working/building/REAL300000003883 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/999 `/scratch/stefan/7769584/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)CCC1CC(=O)[O-]) `REAL300000003883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003883 none CC1C(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)CCC1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 5, 1, 11, 11, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 155, 155, 41, 155, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 201, 201, 201, 168, 168, 168, 168, 155, 41, 41, 1, 1, 1, 168, 168, 168, 168, 168, 201, 201] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 646 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003883 none CC1C(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)CCC1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 5, 1, 11, 11, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 21, 98, 168, 168, 135, 168, 168, 168, 168, 1, 1, 1, 1, 5, 8, 8, 2, 2, 2, 1, 3, 21, 21, 168, 168, 168, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 35, 38, 34, 17, 18, 19, 20, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 451 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003883 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003883 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003883/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003883 Building REAL300000003884 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003884' /scratch/stefan/7769584/working/building/REAL300000003884 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003884 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003884/0 /scratch/stefan/7769584/working/building/REAL300000003884 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1000 `/scratch/stefan/7769584/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CS1) `REAL300000003884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003884 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 17, 17, 17, 61, 159, 201, 201, 194, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 17, 61, 61, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 33, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 460 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: REAL300000003884 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 116, 108, 108, 40, 108, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 108, 40, 40, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 485 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003884 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003884 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003884/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003884 Building REAL300000003885 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003885' /scratch/stefan/7769584/working/building/REAL300000003885 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003885 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003885/0 /scratch/stefan/7769584/working/building/REAL300000003885 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1001 `/scratch/stefan/7769584/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003885 none CC1CC(C(=O)[O-])CCC1=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 140, 140, 41, 140, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 41, 41, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 504 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003885 none CC1CC(C(=O)[O-])CCC1=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 38, 124, 201, 201, 153, 175, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 38, 38, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 11, 34, 32, 27, 28, 29, 30, 31] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40]) total number of confs: 550 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003885 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003885 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003885/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003885 Building REAL300000003886 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003886' /scratch/stefan/7769584/working/building/REAL300000003886 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003886 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003886/0 /scratch/stefan/7769584/working/building/REAL300000003886 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1002 `/scratch/stefan/7769584/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)CCC1C(=O)[O-]) `REAL300000003886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003886 none CC1CC(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)CCC1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 156, 156, 45, 156, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 45, 45, 1, 1, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 504 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003886 none CC1CC(=NNC(=O)COC2=CC=C(Cl)C=C2Cl)CCC1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 49, 156, 201, 201, 197, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 7, 49, 49, 201, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 18, 19, 20, 21, 36, 27, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 418 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003886 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003886 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003886/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003886 Building REAL300000003887 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003887' /scratch/stefan/7769584/working/building/REAL300000003887 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003887 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003887/0 /scratch/stefan/7769584/working/building/REAL300000003887 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1003 `/scratch/stefan/7769584/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CN1) `REAL300000003887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003887 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 177, 177, 143, 143, 42, 143, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 177, 143, 42, 42, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 503 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: REAL300000003887 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 51, 150, 201, 201, 192, 201, 201, 201, 201, 1, 1, 1, 7, 13, 51, 51, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 21, 22, 23, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 445 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003887 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003887 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003887/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003887 Building REAL300000003888 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003888' /scratch/stefan/7769584/working/building/REAL300000003888 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003888 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003888/0 /scratch/stefan/7769584/working/building/REAL300000003888 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1004 `/scratch/stefan/7769584/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003888 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 118, 118, 37, 118, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 118, 37, 37, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 576 number of broken/clashed sets: 180 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003888 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 20, 20, 20, 70, 163, 201, 201, 191, 201, 201, 201, 201, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 20, 70, 70, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40]) total number of confs: 507 number of broken/clashed sets: 180 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003888 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003888 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003888/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003888 Building REAL300000003889 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003889' /scratch/stefan/7769584/working/building/REAL300000003889 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003889 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003889/0 /scratch/stefan/7769584/working/building/REAL300000003889 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1005 `/scratch/stefan/7769584/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003889 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 97, 97, 38, 97, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 99, 97, 38, 38, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003889 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 15, 15, 15, 67, 157, 201, 201, 195, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 13, 15, 67, 67, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003889 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003889 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003889/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003889 Building REAL300000003890 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003890' /scratch/stefan/7769584/working/building/REAL300000003890 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003890 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003890/0 /scratch/stefan/7769584/working/building/REAL300000003890 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1006 `/scratch/stefan/7769584/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003890 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 179, 179, 45, 179, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 196, 179, 45, 45, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 519 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003890 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 4, 8, 8, 8, 41, 131, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 4, 8, 41, 41, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 392 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003890 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003890 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003890/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003890 Building REAL300000003891 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003891' /scratch/stefan/7769584/working/building/REAL300000003891 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003891 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003891/0 /scratch/stefan/7769584/working/building/REAL300000003891 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1007 `/scratch/stefan/7769584/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1F) `REAL300000003891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003891 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 111, 111, 107, 107, 38, 107, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 111, 107, 38, 38, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003891 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 46, 126, 201, 201, 159, 201, 201, 201, 201, 1, 1, 1, 1, 1, 7, 11, 46, 46, 201, 201, 201, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003891 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003891 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003891/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003891 Building REAL300000003892 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003892' /scratch/stefan/7769584/working/building/REAL300000003892 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003892 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003892/0 /scratch/stefan/7769584/working/building/REAL300000003892 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1008 `/scratch/stefan/7769584/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1) `REAL300000003892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003892 none O=C([O-])C=CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 155, 155, 155, 135, 135, 134, 134, 39, 134, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 155, 155, 135, 134, 39, 39, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003892 none O=C([O-])C=CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 11, 23, 11, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 25, 91, 155, 155, 127, 155, 155, 155, 155, 1, 11, 11, 1, 1, 4, 5, 25, 25, 155, 155, 155] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003892 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003892 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003892/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003892 Building REAL300000003893 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003893' /scratch/stefan/7769584/working/building/REAL300000003893 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003893 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003893/0 /scratch/stefan/7769584/working/building/REAL300000003893 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1009 `/scratch/stefan/7769584/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003893 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 42, 128, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 128, 42, 42, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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: 488 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: REAL300000003893 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 71, 176, 201, 201, 198, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 9, 71, 71, 201, 201, 201] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 35, 36, 37, 38, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 444 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003893 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003893 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003893/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003893 Building REAL300000003894 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003894' /scratch/stefan/7769584/working/building/REAL300000003894 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003894 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003894/0 /scratch/stefan/7769584/working/building/REAL300000003894 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1010 `/scratch/stefan/7769584/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CN=CC(C(=O)[O-])=C1) `REAL300000003894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003894 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 45, 147, 201, 201, 191, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 5, 9, 45, 45, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 16, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 446 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: REAL300000003894 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 142, 127, 127, 43, 127, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 127, 43, 43, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 514 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003894 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003894 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003894/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003894 Building REAL300000003895 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003895' /scratch/stefan/7769584/working/building/REAL300000003895 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003895 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003895/0 /scratch/stefan/7769584/working/building/REAL300000003895 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1011 `/scratch/stefan/7769584/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=N1) `REAL300000003895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003895 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 114, 114, 98, 98, 40, 98, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 114, 98, 40, 40, 1, 1, 1, 201] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003895 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 65, 165, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 8, 15, 65, 65, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003895 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003895 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003895/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003895 Building REAL300000003896 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003896' /scratch/stefan/7769584/working/building/REAL300000003896 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003896 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003896/0 /scratch/stefan/7769584/working/building/REAL300000003896 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1012 `/scratch/stefan/7769584/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1O) `REAL300000003896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003896 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 135, 135, 130, 130, 41, 130, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 130, 41, 41, 1, 1, 1, 201, 402] 402 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: 914 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003896 none O=C([O-])C1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 54, 155, 201, 201, 189, 194, 201, 201, 201, 1, 1, 1, 1, 1, 6, 10, 54, 54, 201, 201, 201, 1, 2] 402 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003896 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003896 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003896/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003896 Building REAL300000003897 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003897' /scratch/stefan/7769584/working/building/REAL300000003897 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003897 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003897/0 /scratch/stefan/7769584/working/building/REAL300000003897 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1013 `/scratch/stefan/7769584/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1C(=O)[O-]) `REAL300000003897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003897 none CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 178, 170, 170, 44, 170, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 170, 44, 44, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 520 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: REAL300000003897 none CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 5, 31, 117, 201, 201, 154, 160, 201, 201, 201, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 3, 5, 30, 30, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 490 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003897 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003897 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003897/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003897 Building REAL300000003898 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003898' /scratch/stefan/7769584/working/building/REAL300000003898 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003898 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003898/0 /scratch/stefan/7769584/working/building/REAL300000003898 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1014 `/scratch/stefan/7769584/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000003898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003898 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens 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, 13, 13, 13, 62, 167, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 62, 62, 201, 201, 201, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 421 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: REAL300000003898 none CC(=NNC(=O)COC1=CC=C(Cl)C=C1Cl)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens 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, 124, 108, 108, 41, 108, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 124, 191, 201, 201, 201, 201, 201, 124, 124, 124, 108, 41, 41, 1, 1, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 888 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003898 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003898 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003898/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003898 Building REAL300000003899 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003899' /scratch/stefan/7769584/working/building/REAL300000003899 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003899 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003899/0 /scratch/stefan/7769584/working/building/REAL300000003899 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1015 `/scratch/stefan/7769584/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003899 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 162, 162, 48, 162, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 195, 162, 48, 48, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 513 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: REAL300000003899 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 11, 11, 54, 163, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 4, 10, 54, 54, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 414 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003899 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003899 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003899/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003899 Building REAL300000003900 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003900' /scratch/stefan/7769584/working/building/REAL300000003900 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003900 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003900/0 /scratch/stefan/7769584/working/building/REAL300000003900 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1016 `/scratch/stefan/7769584/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003900 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 160, 160, 48, 160, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 160, 48, 48, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 512 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003900 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 11, 11, 11, 54, 158, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 5, 11, 54, 54, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 27, 28] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 418 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003900 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003900 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003900/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003900 Building REAL300000003901 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003901' /scratch/stefan/7769584/working/building/REAL300000003901 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003901 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003901/0 /scratch/stefan/7769584/working/building/REAL300000003901 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1017 `/scratch/stefan/7769584/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1) `REAL300000003901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003901 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 128, 128, 110, 110, 41, 110, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 128, 110, 41, 41, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300000003901 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 17, 17, 17, 52, 128, 201, 201, 161, 181, 201, 201, 201, 1, 2, 2, 2, 1, 6, 17, 52, 52, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003901 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003901 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003901/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003901 Building REAL300000003902 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003902' /scratch/stefan/7769584/working/building/REAL300000003902 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003902 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003902/0 /scratch/stefan/7769584/working/building/REAL300000003902 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1018 `/scratch/stefan/7769584/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003902 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 72, 34, 72, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 72, 72, 34, 34, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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: 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: REAL300000003902 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 46, 138, 201, 201, 183, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 11, 11, 46, 46, 201, 201, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003902 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003902 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003902/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003902 Building REAL300000003903 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003903' /scratch/stefan/7769584/working/building/REAL300000003903 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003903 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003903/0 /scratch/stefan/7769584/working/building/REAL300000003903 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1019 `/scratch/stefan/7769584/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1) `REAL300000003903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003903 none O=C([O-])C1=COC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 134, 134, 102, 102, 40, 102, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 134, 102, 40, 40, 1, 1, 1, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003903 none O=C([O-])C1=COC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 70, 172, 201, 201, 201, 201, 201, 201, 201, 1, 1, 7, 19, 70, 70, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003903 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003903 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003903/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003903 Building REAL300000003904 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003904' /scratch/stefan/7769584/working/building/REAL300000003904 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003904 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003904/0 /scratch/stefan/7769584/working/building/REAL300000003904 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1020 `/scratch/stefan/7769584/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C(C(=O)[O-])=C1) `REAL300000003904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003904 none CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 165, 165, 94, 94, 47, 94, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 165, 94, 47, 47, 1, 1, 1, 179] 179 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 449 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: REAL300000003904 none CC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 24, 111, 179, 179, 163, 177, 179, 179, 179, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 12, 24, 24, 179, 179, 179, 1] 179 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 408 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003904 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003904 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003904/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003904 Building REAL300000003905 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003905' /scratch/stefan/7769584/working/building/REAL300000003905 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003905 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003905/0 /scratch/stefan/7769584/working/building/REAL300000003905 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1021 `/scratch/stefan/7769584/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CC=C1C(=O)[O-]) `REAL300000003905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003905 none COC1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 158, 158, 158, 96, 96, 96, 96, 38, 96, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 201, 201, 201, 201, 201, 158, 96, 96, 38, 38, 1, 1, 1, 158, 158] 201 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 661 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003905 none COC1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 25, 78, 158, 158, 110, 118, 158, 158, 158, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 7, 25, 25, 158, 158, 158, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003905 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003905 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003905/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003905 Building REAL300000003906 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003906' /scratch/stefan/7769584/working/building/REAL300000003906 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003906 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003906/0 /scratch/stefan/7769584/working/building/REAL300000003906 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1022 `/scratch/stefan/7769584/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1) `REAL300000003906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003906 none CC1=C(C(=O)[O-])NC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 125, 125, 113, 113, 41, 113, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 125, 113, 41, 41, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003906 none CC1=C(C(=O)[O-])NC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 15, 15, 15, 40, 118, 201, 201, 162, 201, 201, 201, 201, 1, 2, 2, 2, 1, 7, 15, 40, 40, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 35, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003906 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003906 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003906/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003906 Building REAL300000003907 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003907' /scratch/stefan/7769584/working/building/REAL300000003907 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003907 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003907/0 /scratch/stefan/7769584/working/building/REAL300000003907 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1023 `/scratch/stefan/7769584/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)SC=C1) `REAL300000003907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003907 none O=C([O-])C1=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 193, 193, 178, 178, 43, 178, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 193, 178, 43, 43, 1, 1, 1, 201, 201] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL300000003907 none O=C([O-])C1=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 8, 8, 8, 45, 150, 201, 201, 187, 200, 201, 201, 201, 1, 1, 1, 3, 7, 45, 45, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 20, 21, 22, 30, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003907 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003907 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003907/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003907 Building REAL300000003908 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003908' /scratch/stefan/7769584/working/building/REAL300000003908 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003908 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003908/0 /scratch/stefan/7769584/working/building/REAL300000003908 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1024 `/scratch/stefan/7769584/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CS1) `REAL300000003908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003908 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 188, 188, 147, 147, 42, 147, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 188, 147, 42, 42, 1, 1, 1, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 505 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: REAL300000003908 none O=C([O-])C1=CC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 4, 4, 10, 10, 10, 45, 149, 201, 201, 195, 201, 201, 201, 201, 1, 1, 1, 4, 10, 45, 45, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 423 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003908 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003908 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003908/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003908 Building REAL300000003909 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003909' /scratch/stefan/7769584/working/building/REAL300000003909 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003909 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003909/0 /scratch/stefan/7769584/working/building/REAL300000003909 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1025 `/scratch/stefan/7769584/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1) `REAL300000003909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003909 none O=C([O-])CCC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 193, 103, 103, 103, 103, 96, 96, 96, 96, 36, 96, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 193, 193, 103, 103, 96, 96, 36, 36, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 825 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003909 none O=C([O-])CCC1=CC=C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 12, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 13, 46, 103, 103, 69, 90, 103, 103, 103, 1, 10, 10, 8, 8, 1, 1, 4, 4, 13, 13, 103, 103, 103] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 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/7769584/working/building/REAL300000003909 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003909 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003909/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003909 Building REAL300000003910 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003910' /scratch/stefan/7769584/working/building/REAL300000003910 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003910 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003910/0 /scratch/stefan/7769584/working/building/REAL300000003910 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1026 `/scratch/stefan/7769584/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003910 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 45, 176, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 176, 45, 45, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003910 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 43, 131, 201, 201, 199, 201, 201, 201, 201, 1, 1, 1, 4, 8, 43, 43, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003910 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003910 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003910/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003910 Building REAL300000003911 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003911' /scratch/stefan/7769584/working/building/REAL300000003911 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003911 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003911/0 /scratch/stefan/7769584/working/building/REAL300000003911 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1027 `/scratch/stefan/7769584/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1) `REAL300000003911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003911 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 167, 167, 40, 167, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 171, 167, 40, 40, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 516 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003911 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 8, 8, 8, 37, 132, 201, 201, 191, 199, 201, 201, 201, 1, 1, 1, 4, 8, 37, 37, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 35, 25, 26, 27] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 420 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003911 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003911 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003911/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003911 Building REAL300000003912 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003912' /scratch/stefan/7769584/working/building/REAL300000003912 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003912 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003912/0 /scratch/stefan/7769584/working/building/REAL300000003912 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1028 `/scratch/stefan/7769584/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1C(=O)[O-]) `REAL300000003912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003912 none CC1=NSC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 192, 192, 180, 180, 42, 180, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 192, 180, 42, 42, 1, 1, 1] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003912 none CC1=NSC(C=NNC(=O)COC2=CC=C(Cl)C=C2Cl)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 8, 8, 8, 44, 130, 201, 201, 175, 201, 201, 201, 201, 1, 1, 3, 3, 2, 2, 2, 4, 8, 44, 44, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21] set([6, 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]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003912 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003912 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003912/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003912 Building REAL300000003913 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003913' /scratch/stefan/7769584/working/building/REAL300000003913 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003913 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003913/0 /scratch/stefan/7769584/working/building/REAL300000003913 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1029 `/scratch/stefan/7769584/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl) `REAL300000003913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003913 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 154, 148, 148, 46, 148, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 154, 148, 46, 46, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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: 503 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: REAL300000003913 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)COC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 35, 137, 201, 201, 199, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 4, 6, 35, 35, 201, 201, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 384 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003913 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003913 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003913/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003913 Building REAL300000003914 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003914' /scratch/stefan/7769584/working/building/REAL300000003914 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003914 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003914/0 /scratch/stefan/7769584/working/building/REAL300000003914 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1030 `/scratch/stefan/7769584/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)N3CCOCC3)C=C2[N+](=O)[O-])C1) `REAL300000003914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003914 none O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)N3CCOCC3)C=C2[N+](=O)[O-])C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 95, 95, 12, 12, 39, 39, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 201, 201, 201, 201, 201, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 39, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 516 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003914 none O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)N3CCOCC3)C=C2[N+](=O)[O-])C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 35, 59, 35, 35, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 39, 39, 39, 39, 1, 1, 1, 2, 2, 35, 35, 35, 35, 35, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 1, 35, 35] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 21, 22, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 241 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003914 none O=C([O-])C1CC(N=NC2=CC=C(S(=O)(=O)N3CCOCC3)C=C2[N+](=O)[O-])C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 35, 35, 14, 13, 130, 130, 129, 199, 199, 200, 200, 201, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 35, 35, 199, 199, 199, 199, 200, 201, 201, 200, 35, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 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]) total number of confs: 619 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003914 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003914 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003914/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003914 Building REAL300000003915 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003915' /scratch/stefan/7769584/working/building/REAL300000003915 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003915 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003915/0 /scratch/stefan/7769584/working/building/REAL300000003915 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1031 `/scratch/stefan/7769584/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)C([N+](=O)[O-])=C1) `REAL300000003915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003915 none CCN(CC)S(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 1, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 59, 112, 175, 7, 59, 59, 7, 16, 16, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 16, 16, 16, 16, 16, 181, 181, 181, 181, 181, 175, 175, 175, 175, 175, 16, 16, 1, 1, 1, 1, 1, 1, 16] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44]) total number of confs: 1139 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: REAL300000003915 none CCN(CC)S(=O)(=O)C1=CC=C(N=NC2CC(C(=O)[O-])C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 1, 8, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 23, 55, 1, 8, 8, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 24, 24, 16, 1, 1, 2, 2, 1, 60, 60, 60, 60, 60, 55, 55, 55, 55, 55, 1, 1, 16, 16, 16, 16, 16, 16, 1] 201 rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 44, 21, 22, 25, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 469 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003915 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003915 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003915/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003915 Building REAL300000003916 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003916' /scratch/stefan/7769584/working/building/REAL300000003916 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003916 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003916/0 /scratch/stefan/7769584/working/building/REAL300000003916 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1032 `/scratch/stefan/7769584/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC([N+](=O)[O-])=CC=C1N=NC1CC(C(=O)[O-])C1) `REAL300000003916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003916 none CCN(CC)S(=O)(=O)C1=CC([N+](=O)[O-])=CC=C1N=NC1CC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 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, 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: [134, 78, 53, 78, 123, 22, 53, 53, 22, 22, 13, 13, 22, 22, 22, 22, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 134, 134, 134, 134, 134, 123, 123, 123, 123, 123, 22, 22, 22, 1, 1, 1, 1, 1, 1] 159 rigid atoms, others: [39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 856 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: REAL300000003916 none CCN(CC)S(=O)(=O)C1=CC([N+](=O)[O-])=CC=C1N=NC1CC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 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, 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: [44, 16, 9, 16, 41, 1, 9, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 22, 22, 22, 33, 33, 22, 44, 44, 44, 44, 44, 41, 41, 41, 41, 41, 1, 1, 1, 22, 22, 22, 22, 22, 22] 159 rigid atoms, others: [36, 5, 38, 8, 9, 10, 11, 14, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 7, 12, 13, 18, 19, 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: 380 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003916 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003916 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003916/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003916 Building REAL300000003917 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003917' /scratch/stefan/7769584/working/building/REAL300000003917 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003917 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003917/0 /scratch/stefan/7769584/working/building/REAL300000003917 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1033 `/scratch/stefan/7769584/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCOCC3)=C2)C1) `REAL300000003917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003917 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCOCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 131, 131, 40, 131, 40, 40, 40, 40, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 131, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 40, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 15, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 438 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003917 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCOCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 38, 21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 39, 39, 39, 39, 39, 1, 21, 21, 21, 21, 7, 1, 1, 1, 39, 39, 40, 40, 40, 40, 39, 39, 1, 21, 21] 201 rigid atoms, others: [32, 8, 41, 10, 11, 12, 13, 14, 15, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 172 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003917 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCOCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 19, 21, 21, 107, 107, 107, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 5, 21, 21, 21, 201, 201, 201, 201, 201, 201, 201, 201, 21, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 522 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003917 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003917 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003917/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003917 Building REAL300000003918 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003918' /scratch/stefan/7769584/working/building/REAL300000003918 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003918 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003918/0 /scratch/stefan/7769584/working/building/REAL300000003918 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1034 `/scratch/stefan/7769584/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1) `REAL300000003918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003918 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 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, 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, 32, 33, 33, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 33, 33, 33, 33, 32, 10, 1, 1, 1, 1, 33, 33] 33 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000003918 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 18, 32, 32, 32, 32, 32, 33, 33, 33, 32, 1, 1, 1, 1, 4, 18, 32, 32, 32, 32, 1, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003918 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003918 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003918/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003918 Building REAL300000003919 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003919' /scratch/stefan/7769584/working/building/REAL300000003919 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003919 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003919/0 /scratch/stefan/7769584/working/building/REAL300000003919 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1035 `/scratch/stefan/7769584/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003919 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC(C(F)(F)F)=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.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 54, 54, 54, 27, 54, 54, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 201, 201, 54, 54, 54, 54, 27, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003919 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC(C(F)(F)F)=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.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 42, 78, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 54, 54, 54, 54, 54, 54, 54, 54, 54, 42, 42, 1, 1, 1, 1, 4, 15, 54, 54, 54, 54] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003919 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003919 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003919/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003919 Building REAL300000003920 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003920' /scratch/stefan/7769584/working/building/REAL300000003920 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003920 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003920/0 /scratch/stefan/7769584/working/building/REAL300000003920 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1036 `/scratch/stefan/7769584/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1) `REAL300000003920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003920 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 61, 34, 88, 88, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 88, 88, 201, 201, 88, 88, 34, 10, 1, 1, 1, 1, 88, 88] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 753 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: REAL300000003920 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 88, 88, 88, 88, 88, 89, 89, 89, 88, 1, 1, 13, 13, 1, 1, 6, 26, 88, 88, 88, 88, 1, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 231 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003920 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003920 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003920/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003920 Building REAL300000003921 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003921' /scratch/stefan/7769584/working/building/REAL300000003921 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003921 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003921/0 /scratch/stefan/7769584/working/building/REAL300000003921 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1037 `/scratch/stefan/7769584/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1)C(=O)[O-]) `REAL300000003921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003921 none CC(OC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 58, 58, 57, 58, 58, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 58, 201, 201, 201, 201, 201, 201, 201, 57, 58, 58, 23, 6, 1, 1, 1, 1, 58] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 453 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: REAL300000003921 none CC(OC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 29, 43, 43, 29, 29, 29, 29, 1, 1, 1, 7, 18, 58, 58, 58, 58, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 38, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 240 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003921 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003921 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003921/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003921 Building REAL300000003922 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003922' /scratch/stefan/7769584/working/building/REAL300000003922 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003922 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003922/0 /scratch/stefan/7769584/working/building/REAL300000003922 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1038 `/scratch/stefan/7769584/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1) `REAL300000003922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003922 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 182, 134, 60, 60, 59, 60, 60, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 60, 201, 201, 182, 182, 59, 60, 60, 19, 6, 1, 1, 1, 1, 60] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 557 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: REAL300000003922 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 26, 36, 18, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 60, 60, 16, 60, 60, 60, 60, 60, 60, 1, 26, 26, 18, 18, 1, 1, 1, 7, 16, 60, 60, 16, 60, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 24, 38, 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, 37]) total number of confs: 308 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003922 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003922 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003922/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003922 Building REAL300000003923 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003923' /scratch/stefan/7769584/working/building/REAL300000003923 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003923 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003923/0 /scratch/stefan/7769584/working/building/REAL300000003923 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1039 `/scratch/stefan/7769584/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1[N+](=O)[O-]) `REAL300000003923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003923 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 3, 3, 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, 28, 27, 39, 39, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 39, 39, 39, 39, 39, 47, 47, 39, 39, 18, 6, 1, 1, 1, 1, 39] 47 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) 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: REAL300000003923 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 17, 39, 39, 39, 39, 1] 47 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 24, 29, 30, 37] 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, 36]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003923 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003923 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003923/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003923 Building REAL300000003924 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003924' /scratch/stefan/7769584/working/building/REAL300000003924 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003924 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003924/0 /scratch/stefan/7769584/working/building/REAL300000003924 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1040 `/scratch/stefan/7769584/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1) `REAL300000003924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003924 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 58, 58, 57, 58, 58, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 58, 201, 201, 57, 58, 58, 26, 10, 1, 1, 1, 1, 58] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 594 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: REAL300000003924 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 34, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 58, 58, 17, 58, 58, 58, 58, 58, 58, 1, 19, 19, 1, 1, 1, 7, 17, 58, 58, 17, 58, 1] 201 rigid atoms, others: [35, 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, 34]) total number of confs: 261 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003924 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003924 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003924/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003924 Building REAL300000003925 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003925' /scratch/stefan/7769584/working/building/REAL300000003925 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003925 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003925/0 /scratch/stefan/7769584/working/building/REAL300000003925 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1041 `/scratch/stefan/7769584/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C(OCC(=O)[O-])=C1) `REAL300000003925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003925 none COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 38, 19, 38, 38, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 38, 38, 107, 197, 201, 201, 38, 59, 59, 59, 38, 38, 19, 7, 1, 1, 1, 1, 197, 197, 38] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 724 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003925 none COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 5, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 8, 38, 57, 57, 1, 3, 3, 3, 1, 1, 4, 8, 38, 38, 38, 38, 38, 38, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 19, 20, 25, 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, 38]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003925 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003925 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003925/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003925 Building REAL300000003926 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003926' /scratch/stefan/7769584/working/building/REAL300000003926 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003926 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003926/0 /scratch/stefan/7769584/working/building/REAL300000003926 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1042 `/scratch/stefan/7769584/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1) `REAL300000003926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003926 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 201, 201, 37, 19, 58, 58, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 58, 58, 58, 58, 19, 6, 1, 1, 1, 1, 58, 58] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003926 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 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] 0 hydrogens 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, 28, 42, 7, 28, 28, 1, 1, 1, 1, 1, 1, 6, 6, 15, 58, 58, 58, 58, 58, 59, 59, 59, 58, 1, 1, 1, 1, 6, 15, 58, 58, 58, 58, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003926 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003926 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003926/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003926 Building REAL300000003927 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003927' /scratch/stefan/7769584/working/building/REAL300000003927 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003927 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003927/0 /scratch/stefan/7769584/working/building/REAL300000003927 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1043 `/scratch/stefan/7769584/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003927 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', '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, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 75, 75, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 75, 75, 75, 75, 48, 10, 1, 1, 1, 1] 75 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28]) 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: REAL300000003927 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', '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, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 11, 11, 47, 75, 75, 63, 75, 75, 75, 75, 75, 75, 2, 2, 2, 1, 11, 47, 75, 75, 75, 75] 75 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, 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/7769584/working/building/REAL300000003927 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003927 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003927/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003927 Building REAL300000003928 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003928' /scratch/stefan/7769584/working/building/REAL300000003928 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003928 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003928/0 /scratch/stefan/7769584/working/building/REAL300000003928 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1044 `/scratch/stefan/7769584/working/3D/1044' -> `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=CC(C(F)(F)F)=C2)C=C1) `REAL300000003928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003928 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 88, 88, 88, 88, 88, 88, 55, 12, 1, 1, 1, 1, 88, 88] 88 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003928 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 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, 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, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 28, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 4, 4, 4, 1, 10, 28, 88, 88, 88, 88, 1, 1] 88 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 25, 26, 38, 30, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003928 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003928 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003928/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003928 Building REAL300000003929 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003929' /scratch/stefan/7769584/working/building/REAL300000003929 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003929 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003929/0 /scratch/stefan/7769584/working/building/REAL300000003929 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1045 `/scratch/stefan/7769584/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC(C(F)(F)F)=C3)=C2C=C1) `REAL300000003929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003929 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 6, 7, 6, 7, 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, 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, 49, 49, 49, 49, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 49, 50, 50, 49, 50, 40, 10, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000003929 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 6, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 8, 25, 50, 50, 50, 49, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 22, 23, 24, 25, 26] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003929 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003929/1 /scratch/stefan/7769584/working/building/REAL300000003929 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1046 `/scratch/stefan/7769584/working/3D/1046' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=CC(C(F)(F)F)=C3)=NNC2=C1) `REAL300000003929.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003929 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 4, 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, 100, 100, 100, 100, 58, 58, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 100, 100, 100, 100, 100, 100, 58, 12, 1, 1, 1, 1, 100, 100] 101 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000003929 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 52, 100, 100, 100, 100, 100, 101, 101, 101, 100, 1, 1, 1, 1, 1, 1, 12, 52, 100, 100, 100, 100, 1, 1] 101 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003929 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003929 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003929/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003929/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003929 Building REAL300000003930 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003930' /scratch/stefan/7769584/working/building/REAL300000003930 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000003930 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003930/0 /scratch/stefan/7769584/working/building/REAL300000003930 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1047 `/scratch/stefan/7769584/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC(C(F)(F)F)=C2)N=N1) `REAL300000003930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003930 none O=C([O-])CN1C=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'H', '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, 1, 5, 15, 15, 15, 1, 8, 8, 7, 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, 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, 53, 53, 53, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 53, 53, 92, 92, 53, 42, 10, 1, 1, 1, 1] 92 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000003930 none O=C([O-])CN1C=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'H', '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, 1, 5, 15, 15, 15, 1, 8, 8, 7, 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, 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: [18, 8, 18, 1, 1, 1, 1, 1, 5, 5, 15, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 8, 8, 1, 5, 15, 53, 53, 53, 53] 92 rigid atoms, others: [3, 4, 5, 6, 7, 20, 21, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003930 /scratch/stefan/7769584/working /scratch/stefan/7769584 mkdir: created directory `1' /scratch/stefan/7769584/working/building/REAL300000003930/1 /scratch/stefan/7769584/working/building/REAL300000003930 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 1 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1048 `/scratch/stefan/7769584/working/3D/1048' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=CC(C(F)(F)F)=C2)N=N1) `REAL300000003930.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000003930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003930 none O=C([O-])CN1C=C(CN=NC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'H', '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, 1, 5, 15, 15, 15, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 126, 126, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 126, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000003930 none O=C([O-])CN1C=C(CN=NC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'H', '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, 1, 5, 15, 15, 15, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 1, 1, 1, 1, 1, 9, 61, 61, 126, 126, 109, 126, 126, 126, 126, 126, 126, 1, 1, 6, 6, 1, 9, 9, 126, 126, 113, 126] 201 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, 30]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003930 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003930 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 1: /scratch/stefan/7769584/working/building/REAL300000003930/1.* 0: /scratch/stefan/7769584/working/building/REAL300000003930/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003930 Building REAL300000003931 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003931' /scratch/stefan/7769584/working/building/REAL300000003931 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003931 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003931/0 /scratch/stefan/7769584/working/building/REAL300000003931 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1049 `/scratch/stefan/7769584/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1OCCC(=O)[O-]) `REAL300000003931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003931 none COC1=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 48, 48, 48, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 48, 48, 47, 47, 118, 181, 183, 201, 199, 78, 78, 78, 48, 14, 6, 1, 1, 1, 1, 48, 48, 181, 181, 183, 183] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 17] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 641 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003931 none COC1=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 48, 48, 15, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 9, 21, 23, 35, 33, 4, 4, 4, 1, 7, 15, 48, 48, 28, 48, 1, 1, 21, 21, 23, 23] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 18, 19, 20, 21, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003931 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003931 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003931/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003931 Building REAL300000003932 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003932' /scratch/stefan/7769584/working/building/REAL300000003932 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003932 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003932/0 /scratch/stefan/7769584/working/building/REAL300000003932 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1050 `/scratch/stefan/7769584/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C(Cl)=C1) `REAL300000003932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003932 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 1, 7, 7, 7, 6, 7, 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, 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, 50, 52, 52, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 52, 52, 52, 52, 52, 36, 10, 1, 1, 1, 1, 52] 52 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003932 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 1, 7, 7, 7, 6, 7, 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, 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, 1, 1, 10, 10, 33, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 10, 33, 52, 52, 52, 52, 1] 52 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003932 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003932 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003932/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003932 Building REAL300000003933 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003933' /scratch/stefan/7769584/working/building/REAL300000003933 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003933 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003933/0 /scratch/stefan/7769584/working/building/REAL300000003933 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1051 `/scratch/stefan/7769584/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1O) `REAL300000003933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003933 none O=C([O-])C1=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [71, 71, 71, 71, 71, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 71, 71, 70, 70, 71, 46, 12, 1, 1, 1, 1, 71, 71, 142] 142 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 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: REAL300000003933 none O=C([O-])C1=CC(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 30, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 9, 30, 71, 71, 71, 71, 1, 1, 2] 142 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 32, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003933 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003933 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003933/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003933 Building REAL300000003934 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003934' /scratch/stefan/7769584/working/building/REAL300000003934 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003934 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003934/0 /scratch/stefan/7769584/working/building/REAL300000003934 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1052 `/scratch/stefan/7769584/working/3D/1052' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1)C(=O)[O-]) `REAL300000003934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003934 none CC(OC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 68, 63, 99, 99, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 99, 99, 39, 10, 1, 1, 1, 1, 99, 99] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 597 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003934 none CC(OC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 6, 6, 29, 99, 99, 99, 99, 99, 100, 100, 100, 99, 1, 1, 14, 22, 22, 14, 14, 14, 14, 1, 1, 6, 29, 99, 99, 99, 99, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 38, 29, 30, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003934 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003934 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003934/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003934 Building REAL300000003935 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003935' /scratch/stefan/7769584/working/building/REAL300000003935 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003935 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003935/0 /scratch/stefan/7769584/working/building/REAL300000003935 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1053 `/scratch/stefan/7769584/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C2=CC=CC=C21) `REAL300000003935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003935 none O=C([O-])CN1C=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C2=CC=CC=C21 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 120, 120, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 120, 121, 121, 121, 120, 120, 201, 201, 121, 38, 10, 1, 1, 1, 1, 121, 121, 121, 120] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: REAL300000003935 none O=C([O-])CN1C=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C2=CC=CC=C21 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 9, 9, 40, 121, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 8, 8, 1, 9, 39, 121, 121, 121, 120, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 35, 20, 21, 22, 23, 24, 25, 38, 28, 37, 36] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003935 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003935 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003935/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003935 Building REAL300000003936 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003936' /scratch/stefan/7769584/working/building/REAL300000003936 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003936 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003936/0 /scratch/stefan/7769584/working/building/REAL300000003936 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1054 `/scratch/stefan/7769584/working/3D/1054' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC(C(F)(F)F)=C2)N1) `REAL300000003936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003936 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC(C(F)(F)F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 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 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, 75, 75, 74, 56, 56, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 74, 75, 75, 75, 75, 56, 12, 1, 1, 1, 1, 74] 75 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003936 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC(C(F)(F)F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 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 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, 3, 3, 1, 1, 1, 6, 6, 24, 75, 75, 36, 75, 75, 75, 75, 75, 75, 1, 2, 2, 2, 1, 6, 23, 75, 75, 47, 74, 1] 75 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003936 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003936 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003936/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003936 Building REAL300000003937 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003937' /scratch/stefan/7769584/working/building/REAL300000003937 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003937 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003937/0 /scratch/stefan/7769584/working/building/REAL300000003937 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1055 `/scratch/stefan/7769584/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1) `REAL300000003937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003937 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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 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, 47, 48, 48, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 48, 47, 48, 48, 42, 12, 1, 1, 1, 1, 48] 48 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003937 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 8, 26, 48, 48, 48, 48, 1] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003937 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003937 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003937/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003937 Building REAL300000003938 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003938' /scratch/stefan/7769584/working/building/REAL300000003938 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003938 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003938/0 /scratch/stefan/7769584/working/building/REAL300000003938 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1056 `/scratch/stefan/7769584/working/3D/1056' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000003938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003938 none CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CC=CC(OCCCC(=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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 6, 18, 28, 43, 57, 57, 1, 9, 9, 9, 20, 33, 33, 33, 33, 1, 1, 1, 18, 18, 28, 28, 43, 43, 1] 201 rigid atoms, others: [1, 35, 36, 37, 44, 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, 38, 39, 40, 41, 42, 43]) total number of confs: 312 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: REAL300000003938 none CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CC=CC(OCCCC(=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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 33, 33, 33, 33, 33, 93, 151, 172, 201, 201, 201, 33, 7, 7, 7, 2, 1, 1, 1, 1, 33, 33, 33, 151, 151, 172, 172, 201, 201, 33] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 13, 31] set([0, 1, 2, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 718 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003938 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003938 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003938/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003938 Building REAL300000003939 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003939' /scratch/stefan/7769584/working/building/REAL300000003939 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003939 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003939/0 /scratch/stefan/7769584/working/building/REAL300000003939 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1057 `/scratch/stefan/7769584/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=C1) `REAL300000003939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003939 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 53, 53, 53, 53, 53, 176, 201, 201, 201, 201, 53, 53, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 28, 28, 28, 28, 53, 53, 53, 53, 53, 53, 201, 201, 201, 201, 53, 53, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 523 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003939 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 11, 23, 23, 30, 30, 1, 1, 6, 24, 24, 53, 53, 41, 53, 53, 53, 53, 53, 53, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 23, 23, 23, 23, 1, 1, 53, 53, 41, 53] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003939 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003939 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003939/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003939 Building REAL300000003940 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003940' /scratch/stefan/7769584/working/building/REAL300000003940 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003940 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003940/0 /scratch/stefan/7769584/working/building/REAL300000003940 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1058) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1058 `/scratch/stefan/7769584/working/3D/1058' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=C1) `REAL300000003940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003940 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 27, 49, 51, 51, 51, 51, 51, 152, 201, 201, 201, 51, 51, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 27, 27, 27, 27, 51, 51, 51, 51, 51, 51, 201, 201, 51, 51, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 612 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: REAL300000003940 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 2, 1, 1, 1, 1, 1, 1, 6, 17, 27, 27, 1, 1, 7, 27, 27, 51, 51, 43, 51, 51, 51, 51, 51, 51, 7, 7, 7, 7, 2, 2, 2, 2, 1, 1, 17, 17, 1, 1, 51, 51, 43, 51] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 39, 13, 14, 40, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003940 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003940 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003940/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003940 Building REAL300000003941 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003941' /scratch/stefan/7769584/working/building/REAL300000003941 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003941 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003941/0 /scratch/stefan/7769584/working/building/REAL300000003941 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1059) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1059 `/scratch/stefan/7769584/working/3D/1059' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000003941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003941 none CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CC=CC(OC(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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 19, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 10, 23, 23, 30, 30, 1, 9, 9, 9, 19, 64, 64, 64, 64, 1, 1, 1, 23, 23, 23, 23, 1] 201 rigid atoms, others: [1, 34, 35, 36, 41, 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, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003941 none CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CC=CC(OC(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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 64, 64, 64, 64, 64, 172, 201, 201, 201, 201, 64, 25, 25, 25, 6, 1, 1, 1, 1, 64, 64, 64, 201, 201, 201, 201, 64] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 13, 30, 31] set([0, 1, 2, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 433 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003941 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003941 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003941/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003941 Building REAL300000003942 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003942' /scratch/stefan/7769584/working/building/REAL300000003942 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003942 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003942/0 /scratch/stefan/7769584/working/building/REAL300000003942 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1060) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1060 `/scratch/stefan/7769584/working/3D/1060' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=C1) `REAL300000003942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003942 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 55, 56, 56, 56, 56, 56, 200, 201, 201, 201, 201, 56, 56, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 33, 33, 33, 33, 55, 55, 56, 56, 56, 56, 201, 201, 201, 201, 56, 56, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 414 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003942 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(C(F)(F)F)=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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 2, 1, 1, 1, 1, 1, 1, 6, 8, 9, 15, 15, 1, 1, 7, 27, 27, 56, 56, 45, 56, 56, 56, 56, 56, 56, 7, 7, 7, 7, 3, 3, 2, 2, 1, 1, 8, 8, 8, 8, 1, 1, 56, 56, 45, 56] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003942 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003942 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003942/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003942 Building REAL300000003943 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003943' /scratch/stefan/7769584/working/building/REAL300000003943 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003943 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003943/0 /scratch/stefan/7769584/working/building/REAL300000003943 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1061) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1061 `/scratch/stefan/7769584/working/3D/1061' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CSC(C(=O)[O-])=C1) `REAL300000003943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003943 none CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CSC(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 14, 1, 1, 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, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 51, 97, 97, 58, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 51, 97, 97, 62, 97, 1, 1] 97 rigid atoms, others: [1, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 274 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003943 none CC(=NNC1=CC=CC(C(F)(F)F)=C1)C1=CSC(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 14, 1, 1, 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, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 42, 97, 97, 97, 97, 97, 97, 97, 43, 43, 43, 12, 1, 1, 1, 1, 97, 97] 97 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 13, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003943 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003943 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003943/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003943 Building REAL300000003944 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003944' /scratch/stefan/7769584/working/building/REAL300000003944 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003944 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003944/0 /scratch/stefan/7769584/working/building/REAL300000003944 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1062) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1062 `/scratch/stefan/7769584/working/3D/1062' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(C(F)(F)F)=C2)C1) `REAL300000003944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003944 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(C(F)(F)F)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [64, 60, 64, 60, 60, 70, 70, 70, 70, 70, 60, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 60, 70, 70, 70, 70, 70, 60, 60, 60, 1, 1, 1, 1, 60, 60] 70 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 171 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003944 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(C(F)(F)F)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 35, 35, 70, 70, 60, 70, 70, 70, 70, 70, 70, 6, 1, 1, 1, 1, 1, 6, 6, 6, 70, 70, 60, 70, 6, 6] 70 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 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: REAL300000003944 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(C(F)(F)F)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 6, 6, 2, 6, 6, 1, 1, 1, 13, 13, 60, 60, 23, 60, 60, 60, 60, 60, 60, 1, 6, 6, 2, 6, 6, 1, 1, 1, 60, 60, 23, 60, 1, 1] 70 rigid atoms, others: [32, 1, 3, 4, 37, 38, 10, 11, 12, 24, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003944 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003944 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003944/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003944 Building REAL300000003945 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003945' /scratch/stefan/7769584/working/building/REAL300000003945 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003945 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003945/0 /scratch/stefan/7769584/working/building/REAL300000003945 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1063) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1063 `/scratch/stefan/7769584/working/3D/1063' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC(C(F)(F)F)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000003945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003945 none CC(N=NC1=CC=CC(C(F)(F)F)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 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, 25, 25, 59, 59, 44, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 4, 4, 4, 4, 59, 59, 52, 59, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 85 rigid atoms, others: [1, 34, 35, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003945 none CC(N=NC1=CC=CC(C(F)(F)F)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 44, 59, 59, 59, 59, 59, 85, 85, 85, 59, 59, 59, 44, 44, 44, 44, 1, 1, 1, 1, 59, 59, 85, 85, 59, 59, 59, 59, 59, 59] 85 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 13, 30, 31] set([0, 1, 2, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003945 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003945 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003945/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003945 Building REAL300000003946 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003946' /scratch/stefan/7769584/working/building/REAL300000003946 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003946 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003946/0 /scratch/stefan/7769584/working/building/REAL300000003946 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1064) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1064 `/scratch/stefan/7769584/working/3D/1064' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=CC(C(F)(F)F)=C1) `REAL300000003946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003946 none CC(CCCCCCC(=O)[O-])N=NC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 85, 97, 116, 124, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 37, 37, 37, 37, 80, 80, 83, 85, 101, 101, 113, 116, 129, 129, 199, 199, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 977 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003946 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003946 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003946/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003946 Building REAL300000003947 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003947' /scratch/stefan/7769584/working/building/REAL300000003947 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003947 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003947/0 /scratch/stefan/7769584/working/building/REAL300000003947 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1065) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1065 `/scratch/stefan/7769584/working/3D/1065' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC(C(F)(F)F)=C1) `REAL300000003947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003947 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 47, 47, 47, 28, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 28, 28, 28, 28, 28, 47, 47, 28, 28, 28, 28, 28, 1, 1, 1, 1] 47 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000003947 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 14, 14, 1, 1, 1, 1, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 9, 9, 1, 1, 1, 1, 1, 28, 28, 28, 28] 47 rigid atoms, others: [0, 1, 2, 3, 32, 33, 7, 8, 9, 10, 25, 26, 29, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003947 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003947 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003947/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003947 Building REAL300000003948 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003948' /scratch/stefan/7769584/working/building/REAL300000003948 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003948 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003948/0 /scratch/stefan/7769584/working/building/REAL300000003948 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1066) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1066 `/scratch/stefan/7769584/working/3D/1066' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC(C(F)(F)F)=C1) `REAL300000003948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003948 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 8, 41, 67, 90, 90, 90, 90, 90, 90, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 41, 41, 41, 41, 67, 67, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1] 90 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 347 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: REAL300000003948 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 7, 1, 1, 1, 3, 3, 1, 1, 1, 14, 46, 46, 90, 90, 90, 90, 90, 90, 90, 90, 90, 14, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90] 90 rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003948 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003948 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003948/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003948 Building REAL300000003949 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003949' /scratch/stefan/7769584/working/building/REAL300000003949 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000003949 as failed and skipping /scratch/stefan/7769584/working /scratch/stefan/7769584 `/scratch/stefan/7769584/working/building/REAL300000003949' -> `/scratch/stefan/7769584/failed/REAL300000003949' Building REAL300000003950 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003950' /scratch/stefan/7769584/working/building/REAL300000003950 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003950 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003950/0 /scratch/stefan/7769584/working/building/REAL300000003950 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1067) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1067 `/scratch/stefan/7769584/working/3D/1067' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003950 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 109, 109, 109, 109, 109, 109, 109, 109, 46, 10, 1, 1, 1, 1] 109 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000003950 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 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, 2, 2, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 63, 109, 109, 109, 109, 109, 109, 109, 109, 109, 2, 2, 2, 1, 2, 2, 2, 1, 13, 63, 109, 109, 109, 109] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003950 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003950 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003950/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003950 Building REAL300000003951 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003951' /scratch/stefan/7769584/working/building/REAL300000003951 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003951 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003951/0 /scratch/stefan/7769584/working/building/REAL300000003951 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1068) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1068 `/scratch/stefan/7769584/working/3D/1068' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1Cl) `REAL300000003951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003951 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 59, 59, 59, 59, 59, 46, 12, 1, 1, 1, 1] 59 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000003951 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 59, 59, 43, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 6, 24, 59, 59, 59, 59] 59 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003951 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003951 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003951/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003951 Building REAL300000003952 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003952' /scratch/stefan/7769584/working/building/REAL300000003952 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003952 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003952/0 /scratch/stefan/7769584/working/building/REAL300000003952 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1069) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1069 `/scratch/stefan/7769584/working/3D/1069' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1F) `REAL300000003952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003952 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 106, 107, 106, 106, 106, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 106, 106, 106, 106, 106, 52, 12, 1, 1, 1, 1, 106] 107 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003952 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 44, 106, 106, 106, 106, 106, 107, 107, 107, 106, 1, 1, 1, 1, 1, 10, 44, 106, 106, 106, 106, 1] 107 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003952 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003952 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003952/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003952 Building REAL300000003953 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003953' /scratch/stefan/7769584/working/building/REAL300000003953 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003953 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003953/0 /scratch/stefan/7769584/working/building/REAL300000003953 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1070) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1070 `/scratch/stefan/7769584/working/3D/1070' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)O1) `REAL300000003953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003953 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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] 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: [149, 150, 150, 150, 91, 91, 91, 91, 56, 56, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 91, 150, 150, 91, 91, 56, 10, 1, 1, 1, 1] 150 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000003953 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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] 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: [29, 13, 30, 13, 1, 1, 1, 1, 1, 1, 6, 6, 26, 91, 91, 91, 91, 91, 92, 92, 92, 91, 1, 13, 13, 1, 1, 6, 26, 91, 91, 91, 91] 150 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003953 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003953 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003953/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003953 Building REAL300000003954 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003954' /scratch/stefan/7769584/working/building/REAL300000003954 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003954 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003954/0 /scratch/stefan/7769584/working/building/REAL300000003954 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1071) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1071 `/scratch/stefan/7769584/working/3D/1071' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=C1) `REAL300000003954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003954 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 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, 44, 44, 44, 44, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 44, 45, 45, 44, 44, 45, 35, 8, 1, 1, 1, 1, 45] 45 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003954 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 4, 20, 45, 45, 45, 44, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003954 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003954 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003954/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003954 Building REAL300000003955 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003955' /scratch/stefan/7769584/working/building/REAL300000003955 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003955 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003955/0 /scratch/stefan/7769584/working/building/REAL300000003955 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1072) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1072 `/scratch/stefan/7769584/working/3D/1072' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=N1) `REAL300000003955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003955 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 64, 65, 64, 64, 64, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 64, 64, 64, 64, 32, 10, 1, 1, 1, 1, 64] 65 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30]) 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: REAL300000003955 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 32, 64, 64, 64, 64, 64, 65, 65, 65, 64, 1, 1, 1, 1, 6, 32, 64, 64, 64, 64, 1] 65 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003955 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003955 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003955/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003955 Building REAL300000003956 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003956' /scratch/stefan/7769584/working/building/REAL300000003956 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003956 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003956/0 /scratch/stefan/7769584/working/building/REAL300000003956 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1073) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1073 `/scratch/stefan/7769584/working/3D/1073' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1O) `REAL300000003956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003956 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 1 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: [85, 84, 85, 84, 84, 84, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 84, 84, 84, 84, 84, 42, 12, 1, 1, 1, 1, 84, 168] 170 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000003956 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 1 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, 1, 9, 9, 40, 84, 84, 40, 84, 84, 85, 85, 85, 84, 1, 1, 1, 1, 1, 9, 40, 84, 84, 54, 84, 1, 2] 170 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 31] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003956 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003956 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003956/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003956 Building REAL300000003957 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003957' /scratch/stefan/7769584/working/building/REAL300000003957 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003957 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003957/0 /scratch/stefan/7769584/working/building/REAL300000003957 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1074) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1074 `/scratch/stefan/7769584/working/3D/1074' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1C(=O)[O-]) `REAL300000003957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003957 none CC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1C(=O)[O-] 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [91, 91, 91, 91, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 91, 91, 91, 92, 91, 92, 92, 92, 91, 91, 52, 12, 1, 1, 1, 1, 91] 92 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003957 none CC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1C(=O)[O-] 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 33, 91, 91, 91, 91, 91, 92, 92, 92, 91, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 33, 91, 91, 91, 91, 1] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003957 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003957 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003957/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003957 Building REAL300000003958 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003958' /scratch/stefan/7769584/working/building/REAL300000003958 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003958 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003958/0 /scratch/stefan/7769584/working/building/REAL300000003958 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1075) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1075 `/scratch/stefan/7769584/working/3D/1075' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1) `REAL300000003958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003958 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 125, 125, 125, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 125, 60, 12, 1, 1, 1, 1, 125] 125 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 28]) 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: REAL300000003958 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 45, 125, 125, 125, 125, 125, 125, 125, 125, 125, 1, 7, 45, 125, 125, 125, 125, 1] 125 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003958 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003958 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003958/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003958 Building REAL300000003959 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003959' /scratch/stefan/7769584/working/building/REAL300000003959 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003959 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003959/0 /scratch/stefan/7769584/working/building/REAL300000003959 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1076) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1076 `/scratch/stefan/7769584/working/3D/1076' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003959 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 55, 55, 55, 55, 43, 13, 1, 1, 1, 1] 55 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27]) 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: REAL300000003959 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 55, 55, 51, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 8, 27, 55, 55, 54, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003959 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003959 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003959/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003959 Building REAL300000003960 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003960' /scratch/stefan/7769584/working/building/REAL300000003960 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003960 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003960/0 /scratch/stefan/7769584/working/building/REAL300000003960 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1077) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1077 `/scratch/stefan/7769584/working/3D/1077' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1O) `REAL300000003960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003960 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 94, 94, 94, 94, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 94, 201, 201, 201, 201, 201, 94, 94, 48, 10, 1, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 690 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003960 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 24, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 32, 94, 94, 42, 94, 94, 94, 94, 94, 94, 1, 13, 13, 12, 12, 13, 1, 1, 8, 32, 94, 94, 47, 94, 13, 13, 26] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000003960 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 119, 201, 201, 148, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 45, 119, 201, 201, 160, 201, 1, 1, 2] 402 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, 39]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003960 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003960 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003960/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003960 Building REAL300000003961 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003961' /scratch/stefan/7769584/working/building/REAL300000003961 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003961 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003961/0 /scratch/stefan/7769584/working/building/REAL300000003961 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1078) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1078 `/scratch/stefan/7769584/working/3D/1078' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003961 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 54, 54, 54, 54, 54, 43, 12, 1, 1, 1, 1] 54 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003961 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 27, 54, 54, 54, 54, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 8, 27, 54, 54, 54, 54] 54 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 25, 26] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003961 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003961 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003961/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003961 Building REAL300000003962 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003962' /scratch/stefan/7769584/working/building/REAL300000003962 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003962 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003962/0 /scratch/stefan/7769584/working/building/REAL300000003962 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1079) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1079 `/scratch/stefan/7769584/working/3D/1079' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003962 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(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', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 8, 1, 1, 1, 1] 27 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300000003962 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(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', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 2, 2, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 16, 27, 27, 16, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 16, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 10, 11, 12, 7, 33, 31] set([8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003962 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003962 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003962/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003962 Building REAL300000003963 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003963' /scratch/stefan/7769584/working/building/REAL300000003963 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003963 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003963/0 /scratch/stefan/7769584/working/building/REAL300000003963 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1080) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1080 `/scratch/stefan/7769584/working/3D/1080' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)S2)=C1) `REAL300000003963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003963 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 201, 201, 100, 100, 100, 100, 47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 100, 201, 201, 201, 201, 100, 100, 47, 10, 1, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 315 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003963 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 34, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 13, 12, 13, 13, 1, 1, 8, 34, 100, 100, 100, 100, 13] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003963 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 52, 52, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 13, 13, 52, 129, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003963 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003963 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003963/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003963 Building REAL300000003964 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003964' /scratch/stefan/7769584/working/building/REAL300000003964 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003964 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003964/0 /scratch/stefan/7769584/working/building/REAL300000003964 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1081) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1081 `/scratch/stefan/7769584/working/3D/1081' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003964 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 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] 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: [158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 62, 62, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 159, 159, 159, 158, 158, 158, 62, 12, 1, 1, 1, 1] 159 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300000003964 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 69, 158, 158, 158, 158, 158, 159, 159, 159, 158, 4, 4, 4, 1, 1, 1, 12, 69, 158, 158, 158, 158] 159 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003964 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003964 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003964/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003964 Building REAL300000003965 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003965' /scratch/stefan/7769584/working/building/REAL300000003965 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003965 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003965/0 /scratch/stefan/7769584/working/building/REAL300000003965 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1082) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1082 `/scratch/stefan/7769584/working/3D/1082' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=C1) `REAL300000003965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003965 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 49, 49, 49, 49, 49, 40, 10, 1, 1, 1, 1, 49] 49 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003965 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 49, 49, 24, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 6, 24, 49, 49, 35, 49, 1] 49 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/7769584/working/building/REAL300000003965 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003965 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003965/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003965 Building REAL300000003966 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003966' /scratch/stefan/7769584/working/building/REAL300000003966 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003966 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003966/0 /scratch/stefan/7769584/working/building/REAL300000003966 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1083) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1083 `/scratch/stefan/7769584/working/3D/1083' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1) `REAL300000003966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003966 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 95, 95, 95, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 95, 95, 95, 48, 10, 1, 1, 1, 1, 95] 95 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 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: REAL300000003966 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 46, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 12, 46, 95, 95, 95, 95, 1] 95 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003966 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003966 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003966/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003966 Building REAL300000003967 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003967' /scratch/stefan/7769584/working/building/REAL300000003967 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003967 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003967/0 /scratch/stefan/7769584/working/building/REAL300000003967 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1084) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1084 `/scratch/stefan/7769584/working/3D/1084' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1C(=O)[O-]) `REAL300000003967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003967 none COC1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1C(=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 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, 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, 176, 176, 176, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 176, 176, 175, 175, 201, 201, 201, 201, 201, 176, 61, 12, 1, 1, 1, 1, 176, 176] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000003967 none COC1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1C(=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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 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, 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, 12, 12, 55, 176, 176, 55, 176, 176, 176, 176, 176, 176, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 12, 55, 176, 176, 55, 176, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003967 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003967 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003967/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003967 Building REAL300000003968 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003968' /scratch/stefan/7769584/working/building/REAL300000003968 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003968 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003968/0 /scratch/stefan/7769584/working/building/REAL300000003968 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1085) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1085 `/scratch/stefan/7769584/working/3D/1085' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C(F)=C1) `REAL300000003968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003968 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 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: [47, 38, 48, 40, 48, 48, 48, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 48, 48, 48, 48, 37, 11, 1, 1, 1, 1, 48] 48 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003968 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 6, 28, 49, 49, 49, 49, 1] 49 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003968 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003968 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003968/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003968 Building REAL300000003969 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003969' /scratch/stefan/7769584/working/building/REAL300000003969 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003969 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003969/0 /scratch/stefan/7769584/working/building/REAL300000003969 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1086) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1086 `/scratch/stefan/7769584/working/3D/1086' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1) `REAL300000003969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003969 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 97, 97, 97, 97, 97, 48, 10, 1, 1, 1, 1, 97] 97 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003969 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 39, 97, 97, 71, 97, 97, 97, 97, 97, 97, 1, 2, 2, 2, 1, 7, 39, 97, 97, 73, 97, 1] 97 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003969 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003969 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003969/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003969 Building REAL300000003970 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003970' /scratch/stefan/7769584/working/building/REAL300000003970 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003970 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003970/0 /scratch/stefan/7769584/working/building/REAL300000003970 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1087) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1087 `/scratch/stefan/7769584/working/3D/1087' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1O) `REAL300000003970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003970 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 206 conformations in input total number of sets (complete confs): 206 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 103, 103, 103, 103, 103, 103, 103, 44, 11, 1, 1, 1, 1, 206] 206 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 367 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003970 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(C(F)(F)F)=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 206 conformations in input total number of sets (complete confs): 206 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 9, 35, 103, 103, 103, 103, 2] 206 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003970 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003970 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003970/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003970 Building REAL300000003971 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003971' /scratch/stefan/7769584/working/building/REAL300000003971 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003971 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003971/0 /scratch/stefan/7769584/working/building/REAL300000003971 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1088) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1088 `/scratch/stefan/7769584/working/3D/1088' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C=C2)=C1) `REAL300000003971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003971 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 143, 143, 70, 143, 139, 58, 38, 97, 97, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 97, 97, 139, 201, 201, 74, 143, 139, 97, 97, 38, 10, 1, 1, 1, 1, 97, 97, 139] 201 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 950 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003971 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 97, 97, 97, 97, 97, 98, 98, 98, 97, 1, 1, 3, 5, 5, 2, 3, 3, 1, 1, 9, 42, 97, 97, 97, 97, 1, 1, 3] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 43, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003971 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 18, 18, 68, 143, 143, 143, 143, 143, 143, 143, 143, 143, 3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 18, 68, 143, 143, 143, 143, 3, 3, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 44, 28, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003971 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003971 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003971/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003971 Building REAL300000003972 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003972' /scratch/stefan/7769584/working/building/REAL300000003972 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003972 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003972/0 /scratch/stefan/7769584/working/building/REAL300000003972 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1089) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1089 `/scratch/stefan/7769584/working/3D/1089' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CS1) `REAL300000003972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003972 none O=C([O-])C1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', '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, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 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, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 53, 53, 53, 42, 12, 1, 1, 1, 1, 53] 53 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003972 none O=C([O-])C1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', '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, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 25, 53, 53, 25, 53, 53, 53, 53, 53, 53, 1, 1, 1, 7, 25, 53, 53, 30, 53, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003972 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003972 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003972/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003972 Building REAL300000003973 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003973' /scratch/stefan/7769584/working/building/REAL300000003973 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003973 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003973/0 /scratch/stefan/7769584/working/building/REAL300000003973 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1090) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1090 `/scratch/stefan/7769584/working/3D/1090' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1OCC(=O)[O-]) `REAL300000003973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003973 none CCOC1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 30, 30, 30, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 30, 30, 30, 30, 113, 192, 195, 195, 83, 83, 83, 83, 83, 30, 10, 6, 1, 1, 1, 1, 31, 31, 192, 192] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003973 none CCOC1=CC(C=NNC2=CC=CC(C(F)(F)F)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 6, 6, 12, 31, 31, 13, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 7, 30, 56, 56, 17, 17, 17, 17, 17, 1, 6, 12, 31, 31, 13, 30, 1, 1, 30, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003973 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003973 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003973/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003973 Building REAL300000003974 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003974' /scratch/stefan/7769584/working/building/REAL300000003974 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003974 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003974/0 /scratch/stefan/7769584/working/building/REAL300000003974 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1091) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1091 `/scratch/stefan/7769584/working/3D/1091' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)O1) `REAL300000003974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003974 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 166, 81, 81, 81, 81, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 81, 201, 201, 166, 166, 81, 81, 45, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003974 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 22, 9, 1, 1, 1, 1, 1, 1, 6, 6, 21, 81, 81, 81, 81, 81, 82, 82, 82, 81, 1, 19, 19, 9, 9, 1, 1, 6, 21, 81, 81, 81, 81] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003974 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003974 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003974/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003974 Building REAL300000003975 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003975' /scratch/stefan/7769584/working/building/REAL300000003975 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003975 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003975/0 /scratch/stefan/7769584/working/building/REAL300000003975 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1092) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1092 `/scratch/stefan/7769584/working/3D/1092' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=CC=C1) `REAL300000003975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003975 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 75, 76, 75, 75, 75, 75, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 75, 76, 76, 76, 75, 76, 50, 12, 1, 1, 1, 1, 76, 76, 76] 76 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003975 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 1, 1, 8, 8, 37, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 8, 36, 76, 76, 76, 75, 1, 1, 1] 76 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 35, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003975 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003975 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003975/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003975 Building REAL300000003976 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003976' /scratch/stefan/7769584/working/building/REAL300000003976 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003976 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003976/0 /scratch/stefan/7769584/working/building/REAL300000003976 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1093) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1093 `/scratch/stefan/7769584/working/3D/1093' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=CC(C(F)(F)F)=C3)=CC=C2O1) `REAL300000003976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003976 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC(C(F)(F)F)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 69, 69, 68, 69, 69, 69, 44, 12, 1, 1, 1, 1, 69, 69] 69 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000003976 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC(C(F)(F)F)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 27, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 7, 27, 69, 69, 69, 69, 1, 1] 69 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003976 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003976 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003976/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003976 Building REAL300000003977 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003977' /scratch/stefan/7769584/working/building/REAL300000003977 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003977 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003977/0 /scratch/stefan/7769584/working/building/REAL300000003977 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1094) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1094 `/scratch/stefan/7769584/working/3D/1094' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(C(F)(F)F)=C3)=CC=CN12) `REAL300000003977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003977 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(C(F)(F)F)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 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, 44, 45, 44, 44, 44, 44, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 44, 44, 44, 44, 44, 42, 12, 1, 1, 1, 1, 44, 44, 44] 45 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000003977 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(C(F)(F)F)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 19, 44, 44, 44, 44, 44, 45, 45, 45, 44, 1, 1, 1, 1, 1, 3, 19, 44, 44, 44, 44, 1, 1, 1] 45 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003977 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003977 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003977/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003977 Building REAL300000003978 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003978' /scratch/stefan/7769584/working/building/REAL300000003978 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003978 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003978/0 /scratch/stefan/7769584/working/building/REAL300000003978 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1095) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1095 `/scratch/stefan/7769584/working/3D/1095' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1Cl) `REAL300000003978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003978 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 67, 38, 67, 67, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 67, 67, 67, 201, 201, 67, 67, 22, 6, 1, 1, 1, 1, 67] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 614 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003978 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(C(F)(F)F)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 52, 7, 1, 1, 1, 1, 1, 1, 6, 6, 16, 67, 67, 67, 67, 67, 68, 68, 68, 67, 1, 1, 1, 32, 32, 1, 1, 6, 16, 67, 67, 67, 67, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003978 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003978 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003978/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003978 Building REAL300000003979 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003979' /scratch/stefan/7769584/working/building/REAL300000003979 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003979 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003979/0 /scratch/stefan/7769584/working/building/REAL300000003979 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1096) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1096 `/scratch/stefan/7769584/working/3D/1096' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C(F)=CC=C2S1) `REAL300000003979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003979 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 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, 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: [85, 84, 85, 84, 84, 84, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 84, 84, 84, 84, 84, 84, 84, 44, 10, 1, 1, 1, 1, 84, 84] 85 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000003979 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(C(F)(F)F)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', '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, 1, 5, 15, 15, 15, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 45, 84, 84, 84, 84, 84, 85, 85, 85, 84, 1, 1, 1, 1, 1, 1, 1, 12, 45, 84, 84, 84, 84, 1, 1] 85 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 20, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003979 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003979 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003979/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003979 Building REAL300000003980 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003980' /scratch/stefan/7769584/working/building/REAL300000003980 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003980 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003980/0 /scratch/stefan/7769584/working/building/REAL300000003980 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1097) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1097 `/scratch/stefan/7769584/working/3D/1097' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC(C(F)(F)F)=C1) `REAL300000003980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003980 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 63, 63, 63, 63, 63, 63, 46, 12, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300000003980 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 63, 63, 63, 63, 63, 63, 63, 63, 63, 4, 4, 4, 1, 1, 1, 8, 26, 63, 63, 63, 63] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003980 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003980 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003980/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003980 Building REAL300000003981 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003981' /scratch/stefan/7769584/working/building/REAL300000003981 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003981 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003981/0 /scratch/stefan/7769584/working/building/REAL300000003981 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1098) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1098 `/scratch/stefan/7769584/working/3D/1098' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(C(F)(F)F)=C3)=N2)C1) `REAL300000003981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003981 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(C(F)(F)F)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 79, 201, 79, 79, 79, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 79, 201, 201, 201, 79, 79, 53, 10, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 475 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003981 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(C(F)(F)F)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 23, 12, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 20, 79, 79, 36, 79, 79, 80, 80, 80, 79, 1, 12, 12, 12, 1, 1, 4, 20, 79, 79, 35, 79, 12, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 281 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: REAL300000003981 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(C(F)(F)F)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 33, 33, 98, 201, 201, 150, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 12, 12, 33, 98, 201, 201, 150, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 514 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003981 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003981 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003981/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003981 Building REAL300000003982 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003982' /scratch/stefan/7769584/working/building/REAL300000003982 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003982 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003982/0 /scratch/stefan/7769584/working/building/REAL300000003982 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1099) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1099 `/scratch/stefan/7769584/working/3D/1099' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)=C1) `REAL300000003982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003982 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', '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, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 170, 129, 170, 191, 41, 129, 129, 41, 41, 41, 41, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 192, 192, 192, 192, 192, 191, 191, 191, 191, 191, 41, 41, 41, 12, 6, 1, 1, 1, 41] 201 rigid atoms, others: [42, 43, 44, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45]) total number of confs: 838 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003982 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC=C(C(=O)[O-])N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', '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, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 18, 8, 18, 37, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 41, 41, 41, 41, 41, 41, 41, 1, 35, 35, 35, 35, 35, 37, 37, 37, 37, 37, 1, 1, 1, 5, 19, 41, 41, 41, 1] 201 rigid atoms, others: [5, 38, 39, 8, 9, 10, 11, 12, 13, 45, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003982 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003982 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003982/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003982 Building REAL300000003983 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003983' /scratch/stefan/7769584/working/building/REAL300000003983 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003983 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003983/0 /scratch/stefan/7769584/working/building/REAL300000003983 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1100) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1100 `/scratch/stefan/7769584/working/3D/1100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])C2)=C1) `REAL300000003983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003983 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 122, 73, 122, 175, 13, 73, 73, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 13, 173, 173, 173, 173, 173, 175, 175, 175, 175, 175, 13, 13, 13, 3, 1, 1, 1, 1, 1, 13] 201 rigid atoms, others: [39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 1044 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003983 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=C2CC(C(=O)[O-])C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 8, 17, 32, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 25, 25, 13, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 5, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 13, 44, 24, 37] set([0, 1, 2, 3, 4, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003983 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003983 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003983/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003983 Building REAL300000003984 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003984' /scratch/stefan/7769584/working/building/REAL300000003984 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003984 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003984/0 /scratch/stefan/7769584/working/building/REAL300000003984 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1101) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1101 `/scratch/stefan/7769584/working/3D/1101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)=C1) `REAL300000003984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003984 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 149, 107, 149, 184, 23, 107, 107, 23, 23, 23, 23, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 194, 194, 194, 194, 194, 184, 184, 184, 184, 184, 23, 23, 23, 7, 5, 1, 1, 1, 23] 201 rigid atoms, others: [42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45]) total number of confs: 943 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: REAL300000003984 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CNC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 20, 51, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 23, 23, 23, 23, 23, 23, 23, 1, 53, 53, 53, 53, 53, 51, 51, 51, 51, 51, 1, 1, 1, 5, 13, 23, 23, 23, 1] 201 rigid atoms, others: [5, 38, 39, 8, 9, 10, 11, 12, 13, 45, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003984 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003984 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003984/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003984 Building REAL300000003985 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003985' /scratch/stefan/7769584/working/building/REAL300000003985 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003985 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003985/0 /scratch/stefan/7769584/working/building/REAL300000003985 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1102) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1102 `/scratch/stefan/7769584/working/3D/1102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)=C1) `REAL300000003985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003985 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 171, 131, 171, 190, 46, 131, 131, 46, 46, 46, 46, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 189, 189, 189, 189, 189, 190, 190, 190, 190, 190, 46, 46, 46, 15, 7, 1, 1, 46] 201 rigid atoms, others: [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, 38, 39, 40, 41, 44]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003985 none CCN(CC)S(=O)(=O)C1=CC=CC(C(=O)NN=CC2=CC(C(=O)[O-])=CO2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 12, 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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens 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, 18, 8, 18, 35, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 46, 46, 46, 46, 46, 46, 46, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 5, 18, 46, 46, 1] 201 rigid atoms, others: [5, 38, 39, 8, 9, 10, 11, 12, 13, 44, 26, 37] set([0, 1, 2, 3, 4, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003985 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003985 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003985/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003985 Building REAL300000003986 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003986' /scratch/stefan/7769584/working/building/REAL300000003986 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003986 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003986/0 /scratch/stefan/7769584/working/building/REAL300000003986 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1103) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1103 `/scratch/stefan/7769584/working/3D/1103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)N1) `REAL300000003986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003986 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 155, 155, 75, 75, 30, 75, 30, 30, 30, 30, 6, 1, 6, 6, 1, 1, 1, 1, 1, 30, 201, 201, 201, 155, 75, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 30, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43]) total number of confs: 393 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003986 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 29, 29, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 30, 30, 30, 30, 1, 85, 85, 85, 29, 5, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 1, 85] 201 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 25, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 43]) 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: REAL300000003986 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 34, 85, 85, 34, 85, 85, 201, 201, 201, 201, 201, 201, 201, 85, 1, 1, 1, 9, 34, 85, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 85, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 831 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003986 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003986 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003986/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003986 Building REAL300000003987 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003987' /scratch/stefan/7769584/working/building/REAL300000003987 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003987 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003987/0 /scratch/stefan/7769584/working/building/REAL300000003987 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1104) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1104 `/scratch/stefan/7769584/working/3D/1104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)C1) `REAL300000003987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003987 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 157, 157, 81, 81, 24, 81, 24, 24, 24, 24, 5, 1, 5, 5, 1, 1, 1, 1, 1, 24, 157, 157, 157, 157, 81, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 24, 157, 157] 157 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 321 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003987 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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, 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: [62, 38, 62, 38, 38, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 1, 38, 38, 38, 38, 7, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 1, 38, 38] 157 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 40, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 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: REAL300000003987 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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, 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: [3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 9, 38, 38, 36, 38, 38, 157, 157, 157, 157, 157, 157, 157, 38, 1, 1, 1, 1, 9, 38, 38, 37, 157, 157, 157, 157, 157, 157, 157, 157, 38, 1, 1] 157 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003987 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003987 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003987/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003987 Building REAL300000003988 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003988' /scratch/stefan/7769584/working/building/REAL300000003988 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003988 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003988/0 /scratch/stefan/7769584/working/building/REAL300000003988 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1105) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1105 `/scratch/stefan/7769584/working/3D/1105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=CN1) `REAL300000003988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003988 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 196, 196, 162, 162, 80, 80, 31, 80, 31, 31, 31, 31, 6, 1, 6, 6, 1, 1, 1, 1, 1, 31, 196, 196, 196, 162, 80, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 31, 196, 196] 196 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003988 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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] 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: [81, 81, 81, 81, 81, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 31, 1, 81, 81, 81, 31, 7, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 1, 81, 81] 196 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 41, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) 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: REAL300000003988 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 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] 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, 9, 9, 30, 30, 30, 81, 81, 56, 81, 81, 196, 196, 196, 196, 196, 196, 196, 81, 1, 1, 1, 9, 30, 81, 81, 81, 196, 196, 196, 196, 196, 196, 196, 196, 81, 1, 1] 196 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003988 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003988 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003988/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003988 Building REAL300000003989 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003989' /scratch/stefan/7769584/working/building/REAL300000003989 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003989 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003989/0 /scratch/stefan/7769584/working/building/REAL300000003989 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1106) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1106 `/scratch/stefan/7769584/working/3D/1106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=C1) `REAL300000003989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003989 none O=C([O-])C1=COC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 144, 144, 71, 71, 28, 71, 28, 28, 28, 28, 6, 1, 6, 6, 1, 1, 1, 1, 1, 28, 201, 201, 144, 71, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 28, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003989 none O=C([O-])C1=COC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 29, 29, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 28, 28, 1, 81, 81, 29, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 1, 81] 201 rigid atoms, others: [32, 41, 10, 12, 13, 14, 15, 16, 17, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 42]) 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: REAL300000003989 none O=C([O-])C1=COC(C=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCC3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 33, 33, 33, 81, 81, 52, 81, 81, 201, 201, 201, 201, 201, 201, 201, 81, 1, 1, 9, 33, 81, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 81, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 26, 27] set([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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 797 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003989 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003989 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003989/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003989 Building REAL300000003990 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003990' /scratch/stefan/7769584/working/building/REAL300000003990 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003990 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003990/0 /scratch/stefan/7769584/working/building/REAL300000003990 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1107) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1107 `/scratch/stefan/7769584/working/3D/1107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCCC3)=C2)C1) `REAL300000003990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003990 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 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: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 134, 134, 38, 134, 38, 38, 38, 38, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 38, 201, 201, 201, 201, 134, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 444 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003990 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 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: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 36, 20, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 38, 39, 39, 39, 38, 1, 20, 20, 20, 20, 7, 1, 1, 1, 38, 38, 39, 39, 39, 39, 39, 39, 38, 38, 1, 20, 20] 201 rigid atoms, others: [32, 43, 8, 10, 11, 12, 13, 14, 15, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) 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: REAL300000003990 none O=C([O-])C1CC(=NNC(=O)C2=CC=CC(S(=O)(=O)N3CCCCC3)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 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: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 9, 20, 20, 101, 101, 101, 201, 201, 201, 201, 201, 20, 1, 1, 1, 1, 5, 20, 20, 9, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 20, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003990 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003990 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003990/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003990 Building REAL300000003991 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003991' /scratch/stefan/7769584/working/building/REAL300000003991 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003991 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003991/0 /scratch/stefan/7769584/working/building/REAL300000003991 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1108) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1108 `/scratch/stefan/7769584/working/3D/1108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1Cl) `REAL300000003991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003991 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 145, 54, 54, 54, 25, 54, 54, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 54, 54, 54, 54, 25, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 621 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: REAL300000003991 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 7, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 53, 90, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 54, 54, 26, 54, 54, 54, 53, 53, 1, 1, 1, 1, 5, 26, 54, 54, 26, 54] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 449 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003991 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003991 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003991/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003991 Building REAL300000003992 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003992' /scratch/stefan/7769584/working/building/REAL300000003992 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003992 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003992/0 /scratch/stefan/7769584/working/building/REAL300000003992 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1109) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1109 `/scratch/stefan/7769584/working/3D/1109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000003992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003992 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [44, 3, 44, 45, 77, 85, 85, 77, 85, 85, 85, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 30, 45, 45, 77, 85, 85, 77, 85, 12, 12, 1, 1, 12, 12] 85 rigid atoms, others: [35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 275 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003992 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 62, 62, 33, 62, 62, 62, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 33, 62, 62, 33, 62, 1, 1, 12, 12, 1, 1] 85 rigid atoms, others: [1, 34, 37, 38, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 207 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: REAL300000003992 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 62, 62, 27, 25, 85, 85, 85, 85, 85, 85, 85, 62, 62, 25, 25, 25, 5, 1, 1, 1, 1, 62, 62, 85, 85, 62, 62] 85 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: 254 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003992 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003992 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003992/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003992 Building REAL300000003993 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003993' /scratch/stefan/7769584/working/building/REAL300000003993 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003993 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003993/0 /scratch/stefan/7769584/working/building/REAL300000003993 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1110) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1110 `/scratch/stefan/7769584/working/3D/1110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=O)[O-]) `REAL300000003993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003993 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=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', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 41, 41, 41, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 131, 199, 201, 201, 80, 80, 80, 41, 14, 4, 1, 1, 1, 1, 41, 41, 199, 199] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 583 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003993 none COC1=CC(C=NNC2=CC=CC=C2Cl)=CC=C1OCC(=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', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 41, 41, 23, 41, 41, 41, 1, 1, 1, 1, 9, 43, 68, 68, 3, 3, 3, 1, 7, 23, 41, 41, 23, 41, 1, 1, 43, 43] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 15, 16, 17, 18, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003993 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003993 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003993/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003993 Building REAL300000003994 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003994' /scratch/stefan/7769584/working/building/REAL300000003994 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003994 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003994/0 /scratch/stefan/7769584/working/building/REAL300000003994 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1111) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1111 `/scratch/stefan/7769584/working/3D/1111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1) `REAL300000003994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003994 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 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, 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: [180, 178, 180, 104, 29, 29, 77, 76, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 178, 178, 77, 76, 28, 5, 1, 1, 1, 1, 77, 77] 180 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 32, 31]) total number of confs: 679 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: REAL300000003994 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 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, 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: [32, 16, 32, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 76, 76, 45, 76, 76, 76, 1, 1, 16, 16, 1, 1, 9, 43, 76, 76, 46, 76, 1, 1] 180 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 331 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003994 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003994 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003994/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003994 Building REAL300000003995 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003995' /scratch/stefan/7769584/working/building/REAL300000003995 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003995 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003995/0 /scratch/stefan/7769584/working/building/REAL300000003995 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1112) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1112 `/scratch/stefan/7769584/working/3D/1112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300000003995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003995 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OCC(=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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 41, 68, 68, 41, 68, 68, 68, 1, 1, 1, 1, 1, 1, 6, 22, 39, 39, 1, 11, 11, 11, 41, 68, 68, 41, 68, 1, 1, 1, 22, 22, 1] 201 rigid atoms, others: [32, 1, 35, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 337 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: REAL300000003995 none CC(=NNC1=CC=CC=C1Cl)C1=CC=CC(OCC(=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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 68, 68, 68, 68, 68, 144, 201, 201, 201, 68, 16, 16, 16, 4, 1, 1, 1, 1, 68, 68, 68, 201, 201, 68] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 513 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003995 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003995 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003995/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003995 Building REAL300000003996 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003996' /scratch/stefan/7769584/working/building/REAL300000003996 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003996 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003996/0 /scratch/stefan/7769584/working/building/REAL300000003996 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1113) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1113 `/scratch/stefan/7769584/working/3D/1113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000003996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003996 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 17, 25, 25, 17, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 17, 25, 25, 17, 25, 1, 1, 9, 17, 17, 1, 1] 64 rigid atoms, others: [1, 34, 38, 33, 11, 12, 13, 14, 15, 23, 24, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003996 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 25, 25, 12, 12, 40, 40, 40, 58, 64, 64, 64, 25, 25, 12, 12, 12, 3, 1, 1, 1, 1, 25, 25, 58, 64, 64, 25, 25] 64 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, 39]) total number of confs: 285 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003996 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003996 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003996/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003996 Building REAL300000003997 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003997' /scratch/stefan/7769584/working/building/REAL300000003997 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003997 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003997/0 /scratch/stefan/7769584/working/building/REAL300000003997 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1114) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1114 `/scratch/stefan/7769584/working/3D/1114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1) `REAL300000003997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003997 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 1, 9, 9, 9, 9, 9, 1, 1] 37 rigid atoms, others: [1, 34, 35, 41, 42, 11, 12, 13, 14, 15, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003997 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 8, 8, 17, 17, 17, 37, 37, 37, 37, 37, 9, 9, 8, 8, 8, 3, 1, 1, 1, 1, 9, 9, 37, 37, 37, 37, 37, 9, 9] 37 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 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: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003997 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003997 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003997/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003997 Building REAL300000003998 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003998' /scratch/stefan/7769584/working/building/REAL300000003998 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003998 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003998/0 /scratch/stefan/7769584/working/building/REAL300000003998 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1115) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1115 `/scratch/stefan/7769584/working/3D/1115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1) `REAL300000003998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003998 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)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', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 5, 5, 5, 1, 1] 9 rigid atoms, others: [1, 35, 36, 41, 42, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 23 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003998 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)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', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 3, 3] 9 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, 38, 39, 40, 41, 42]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003998 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003998 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003998/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003998 Building REAL300000003999 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000003999' /scratch/stefan/7769584/working/building/REAL300000003999 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000003999 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000003999/0 /scratch/stefan/7769584/working/building/REAL300000003999 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1116) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1116 `/scratch/stefan/7769584/working/3D/1116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000003999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000003999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000003999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003999 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 23, 23, 21, 23, 23, 23, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 6, 6, 6, 21, 23, 23, 23, 23, 1, 1, 2, 2, 1, 1] 43 rigid atoms, others: [1, 34, 33, 11, 12, 13, 14, 15, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 81 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000003999 none CC(=NNC1=CC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 15, 15, 43, 43, 43, 23, 23, 15, 15, 15, 5, 1, 1, 1, 1, 23, 23, 43, 43, 23, 23] 43 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000003999 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000003999 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000003999/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000003999 Building REAL300000004000 mkdir: created directory `/scratch/stefan/7769584/working/building/REAL300000004000' /scratch/stefan/7769584/working/building/REAL300000004000 /scratch/stefan/7769584/working /scratch/stefan/7769584 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000004000 mkdir: created directory `0' /scratch/stefan/7769584/working/building/REAL300000004000/0 /scratch/stefan/7769584/working/building/REAL300000004000 /scratch/stefan/7769584/working /scratch/stefan/7769584 Protomer 0 (index: 1117) Found valid previously generated 3D confromation in /scratch/stefan/7769584/working/3D/1117 `/scratch/stefan/7769584/working/3D/1117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC=C1Cl)CCC2) `REAL300000004000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000004000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769584/working/building/REAL300000004000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000004000 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC=C1Cl)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 18, 18, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 18, 18, 18, 5, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17] 18 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 37 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: REAL300000004000 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC=C1Cl)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 17, 17, 8, 17, 17, 17, 1, 1, 1, 2, 2, 2, 8, 17, 17, 8, 17, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 34, 19, 20, 21, 35, 30, 31] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769584/working/building/REAL300000004000 /scratch/stefan/7769584/working /scratch/stefan/7769584 Finished preparing REAL300000004000 Recording results /scratch/stefan/7769584/working /scratch/stefan/7769584 Appending to /scratch/stefan/7769584/finished/xaaaaad.* 0: /scratch/stefan/7769584/working/building/REAL300000004000/0.* Removing working files in /scratch/stefan/7769584/working/building/REAL300000004000 /scratch/stefan/7769584 Compressing combined databse files /scratch/stefan/7769584/finished/xaaaaad.db2.gz /scratch/stefan/7769584/finished/xaaaaad.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7769584/finished) ======================================================= Finalizing... removed `/scratch/stefan/7769584/working/3D/1118' removed directory: `/scratch/stefan/7769584/working/3D' `/scratch/stefan/7769584/working/protonate' -> `/scratch/stefan/7769584/archive' `/scratch/stefan/7769584/working/input-smiles.ism' -> `/scratch/stefan/7769584/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7769584/working/building' rmdir: removing directory, `/scratch/stefan/7769584/working' ls: No match. ls: No match.